bio 1.4.1 → 1.4.2

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Files changed (61) hide show
  1. data/ChangeLog +954 -0
  2. data/KNOWN_ISSUES.rdoc +40 -5
  3. data/README.rdoc +36 -35
  4. data/RELEASE_NOTES.rdoc +87 -59
  5. data/bioruby.gemspec +24 -2
  6. data/doc/RELEASE_NOTES-1.4.1.rdoc +104 -0
  7. data/doc/Tutorial.rd +162 -200
  8. data/doc/Tutorial.rd.html +149 -146
  9. data/lib/bio.rb +1 -0
  10. data/lib/bio/appl/blast.rb +1 -1
  11. data/lib/bio/appl/blast/ddbj.rb +26 -34
  12. data/lib/bio/appl/blast/genomenet.rb +21 -11
  13. data/lib/bio/db/embl/sptr.rb +193 -21
  14. data/lib/bio/db/fasta.rb +1 -1
  15. data/lib/bio/db/fastq.rb +14 -0
  16. data/lib/bio/db/fastq/format_fastq.rb +2 -2
  17. data/lib/bio/db/genbank/ddbj.rb +1 -2
  18. data/lib/bio/db/genbank/format_genbank.rb +1 -1
  19. data/lib/bio/db/medline.rb +1 -0
  20. data/lib/bio/db/newick.rb +3 -1
  21. data/lib/bio/db/pdb/pdb.rb +9 -9
  22. data/lib/bio/db/pdb/residue.rb +2 -2
  23. data/lib/bio/io/ddbjrest.rb +344 -0
  24. data/lib/bio/io/ncbirest.rb +121 -1
  25. data/lib/bio/location.rb +2 -2
  26. data/lib/bio/reference.rb +3 -4
  27. data/lib/bio/shell/plugin/entry.rb +7 -3
  28. data/lib/bio/shell/plugin/ncbirest.rb +5 -1
  29. data/lib/bio/util/restriction_enzyme.rb +3 -0
  30. data/lib/bio/util/restriction_enzyme/dense_int_array.rb +195 -0
  31. data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +7 -7
  32. data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +57 -18
  33. data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +2 -2
  34. data/lib/bio/util/restriction_enzyme/sorted_num_array.rb +219 -0
  35. data/lib/bio/version.rb +1 -1
  36. data/sample/test_restriction_enzyme_long.rb +4403 -0
  37. data/test/data/fasta/EFTU_BACSU.fasta +8 -0
  38. data/test/data/genbank/CAA35997.gp +48 -0
  39. data/test/data/genbank/SCU49845.gb +167 -0
  40. data/test/data/litdb/1717226.litdb +13 -0
  41. data/test/data/pir/CRAB_ANAPL.pir +6 -0
  42. data/test/functional/bio/appl/blast/test_remote.rb +93 -0
  43. data/test/functional/bio/appl/test_blast.rb +61 -0
  44. data/test/functional/bio/io/test_ddbjrest.rb +47 -0
  45. data/test/functional/bio/test_command.rb +3 -3
  46. data/test/unit/bio/db/embl/test_sptr.rb +6 -6
  47. data/test/unit/bio/db/embl/test_uniprot_new_part.rb +208 -0
  48. data/test/unit/bio/db/genbank/test_common.rb +274 -0
  49. data/test/unit/bio/db/genbank/test_genbank.rb +401 -0
  50. data/test/unit/bio/db/genbank/test_genpept.rb +81 -0
  51. data/test/unit/bio/db/pdb/test_pdb.rb +3287 -11
  52. data/test/unit/bio/db/test_fasta.rb +34 -12
  53. data/test/unit/bio/db/test_fastq.rb +26 -0
  54. data/test/unit/bio/db/test_litdb.rb +95 -0
  55. data/test/unit/bio/db/test_medline.rb +1 -0
  56. data/test/unit/bio/db/test_nbrf.rb +82 -0
  57. data/test/unit/bio/db/test_newick.rb +22 -4
  58. data/test/unit/bio/test_reference.rb +35 -0
  59. data/test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb +201 -0
  60. data/test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb +281 -0
  61. metadata +44 -38
data/ChangeLog CHANGED
@@ -1,3 +1,957 @@
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+ commit 3acc1e098839cacbe85b5c23367ab14e0c4fe3ea
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 15:01:49 2011 +0900
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+
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+ Preparation for bioruby-1.4.2 release.
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+
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+ bioruby.gemspec | 2 +-
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+ lib/bio/version.rb | 2 +-
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+ 2 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit bf69125192fa01ae3495e094e7ef1b5e895954ad
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 14:42:02 2011 +0900
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+
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+ updated bioruby.gemspec
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+
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+ bioruby.gemspec | 3 +++
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+ 1 files changed, 3 insertions(+), 0 deletions(-)
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+
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+ commit e0a3ead917812199c6a0e495f3afa6a636bbf0c5
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 14:39:54 2011 +0900
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+
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+ Added PLUGIN section to README.rdoc, and some changes made.
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+
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+ README.rdoc | 20 +++++++++++++++++---
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+ 1 files changed, 17 insertions(+), 3 deletions(-)
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+
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+ commit 1da0a1ce6eddcef8f8fc811b0a2cf8d58f880642
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 14:38:13 2011 +0900
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+
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+ updated doc/Tutorial.rd.html
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+
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+ doc/Tutorial.rd.html | 41 ++++++++++++++++++++---------------------
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+ 1 files changed, 20 insertions(+), 21 deletions(-)
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+
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+ commit a8b90367b830e58b397536be3dada10cdde97aab
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 14:36:24 2011 +0900
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+
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+ Removed sections contain obsolete (404 Not Found) URL in Tutorial.rd.
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+
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+ doc/Tutorial.rd | 12 ------------
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+ 1 files changed, 0 insertions(+), 12 deletions(-)
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+
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+ commit e17546cb90a012cd1f51674ceb4c8da5dd516bdf
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+ Author: Michael O'Keefe <okeefm@rpi.edu>
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+ Date: Tue Aug 23 20:15:44 2011 -0400
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+
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+ Updated tutorial
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+
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+ * Updated tutorial
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+ (original commit id: 7b9108657961cf2354278e04971c32059b3ed4e2
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+ and some preceding commits)
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+
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+ doc/Tutorial.rd | 55 ++++++++++++++++++++++++++++++++-----------------------
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+ 1 files changed, 32 insertions(+), 23 deletions(-)
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+
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+ commit de8a394129c752a0b9a5975a73c5eb582d9681d3
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 13:24:27 2011 +0900
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+
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+ fix typo and change order of lines
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+
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+ RELEASE_NOTES.rdoc | 6 +++---
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+ 1 files changed, 3 insertions(+), 3 deletions(-)
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+
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+ commit 1cf2a11199655e4c9f5fc49c5a588b99c18ab7ca
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 13:16:11 2011 +0900
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+
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+ RELEASE_NOTE.rdoc modified to reflect recent changes
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+
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+ RELEASE_NOTES.rdoc | 14 ++++++++++++++
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+ 1 files changed, 14 insertions(+), 0 deletions(-)
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+
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+ commit b44871a5866eeb2d379f080b39b09693c9e9e3cc
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 13:15:14 2011 +0900
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+
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+ In BioRuby Shell, getent() fails when EMBOSS seqret does not found.
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+
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+ lib/bio/shell/plugin/entry.rb | 10 +++++++---
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+ 1 files changed, 7 insertions(+), 3 deletions(-)
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+
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+ commit 179e7506b008a220d5dd42ce1a6c7ce589c3fcda
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 26 12:26:52 2011 +0900
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+
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+ New methods Bio::NCBI::REST::EFetch.nucleotide and protein
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+
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+ * New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
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+ to get data from "nucleotide" and "protein" database respectively.
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+ Because NCBI changed not to accept "gb" format for the database
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+ "sequence", the two new methods are added for convenience.
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+ * In BioRuby Shell, efetch method uses the above new methods.
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+
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+ lib/bio/io/ncbirest.rb | 122 +++++++++++++++++++++++++++++++++++++-
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+ lib/bio/shell/plugin/ncbirest.rb | 6 ++-
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+ 2 files changed, 126 insertions(+), 2 deletions(-)
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+
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+ commit 99b31379bb41c7cad34c1e7dc00f802da37de1cd
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Aug 25 19:03:43 2011 +0900
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+
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+ New method Bio::Fastq#to_s
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+
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+ * New method Bio::Fastq#to_s.
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+ Thanks to Tomoaki NISHIYAMA who wrote a patch.
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+ (https://github.com/bioruby/bioruby/pull/37)
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+
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+ lib/bio/db/fastq.rb | 14 ++++++++++++++
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+ test/unit/bio/db/test_fastq.rb | 14 ++++++++++++++
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+ 2 files changed, 28 insertions(+), 0 deletions(-)
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+
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+ commit 8ab772b37850c3874b55cf37d091046394cda5bd
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Aug 25 15:23:00 2011 +0900
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+
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+ RELEASE_NOTES.rdoc changed to reflect recent changes.
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+
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+ RELEASE_NOTES.rdoc | 16 ++++++++++++++++
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+ 1 files changed, 16 insertions(+), 0 deletions(-)
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+
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+ commit 8db6abdcc81db6a58bdd99e7f8d410b1a74496b1
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Aug 25 14:28:42 2011 +0900
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+
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+ A test connecting to DDBJ BLAST web service is enabled.
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+
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+ test/functional/bio/appl/test_blast.rb | 2 +-
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+ 1 files changed, 1 insertions(+), 1 deletions(-)
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+
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+ commit 121ad93c0c1f018ee389972ac5e5e8cc395f00d1
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Aug 25 14:15:23 2011 +0900
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+
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+ Bio::DDBJ::REST::*. new classes for DDBJ REST web services.
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+
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+ * Bio::DDBJ::REST::*: new classes for DDBJ REST web services (WABI).
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+ Currently not all services are covered. (lib/bio/io/ddbjrest.rb)
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+ * autoload of the above (lib/bio/db/genbank/ddbj.rb, lib/bio.rb)
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+ * Tests for the above (but still incomplete)
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+ (test/functional/bio/io/test_ddbjrest.rb)
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+ * Remote BLAST using DDBJ server now uses REST interface instead
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+ of SOAP, for Ruby 1.9.x support.
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+ (lib/bio/appl/blast/ddbj.rb)
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+
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+ lib/bio.rb | 1 +
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+ lib/bio/appl/blast/ddbj.rb | 33 +---
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+ lib/bio/db/genbank/ddbj.rb | 3 +-
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+ lib/bio/io/ddbjrest.rb | 344 +++++++++++++++++++++++++++++++
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+ test/functional/bio/io/test_ddbjrest.rb | 47 +++++
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+ 5 files changed, 399 insertions(+), 29 deletions(-)
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+ create mode 100644 lib/bio/io/ddbjrest.rb
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+ create mode 100644 test/functional/bio/io/test_ddbjrest.rb
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+
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+ commit 7e8ba7c1388204daa5245d2128d01f6f40298185
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Aug 18 00:08:51 2011 +0900
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+
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+ In Fastq formatter, default width value changed to nil
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+
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+ * In Bio::Sequence#output(:fastq) (Fastq output formatter),
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+ default width value is changed from 70 to nil, which means
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+ "without wrapping". close [Feature #3191]
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+ (https://redmine.open-bio.org/issues/3191)
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+
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+ RELEASE_NOTES.rdoc | 8 ++++++--
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+ lib/bio/db/fastq/format_fastq.rb | 4 ++--
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+ test/unit/bio/db/test_fastq.rb | 12 ++++++++++++
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+ 3 files changed, 20 insertions(+), 4 deletions(-)
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+
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+ commit 0fb65211519febff18413c589fe7af753ee2e61d
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Wed Aug 17 22:02:03 2011 +0900
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+
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+ Bug fix: Bio::SPTR follow-up of UniProtKB format changes
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+
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+ * Bug fix: Bio::SPTR follow-up of UniProtKB format changes.
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+ * Tests are added about the fix.
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+ * Bug fix: Bio::SPTR#cc_web_resource should be private.
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+ * Incompatible changes in Bio::SPTR#cc("WEB RESOURCE") is
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+ documented in RELEASE_NOTES.rdoc.
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+ * KNOWN_ISSUES.rdoc: description about incompleteness of the fix.
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+ * Thanks to Nicholas Letourneau who reports the issue.
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+ (https://github.com/bioruby/bioruby/pull/36)
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+
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+ KNOWN_ISSUES.rdoc | 5 +
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+ RELEASE_NOTES.rdoc | 20 ++-
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+ lib/bio/db/embl/sptr.rb | 214 +++++++++++++++++++++---
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+ test/unit/bio/db/embl/test_sptr.rb | 12 +-
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+ test/unit/bio/db/embl/test_uniprot_new_part.rb | 208 +++++++++++++++++++++++
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+ 5 files changed, 430 insertions(+), 29 deletions(-)
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+ create mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
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+
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+ commit 0d066ab6b8fc19f1cf6e66e07c2065775739cccd
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat Aug 13 00:58:51 2011 +0900
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+
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+ preparation for release: alpha test version 1.4.2-alpha1
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+
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+ bioruby.gemspec | 23 +++++++++++++++++++++--
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+ lib/bio/version.rb | 4 ++--
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+ 2 files changed, 23 insertions(+), 4 deletions(-)
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+
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+ commit 55ece17775f5d24cf62f93d54ded5dc6eed53584
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 12 21:57:25 2011 +0900
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+
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+ Test bug fix: use sort command in PATH
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+
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+ * Test bug fix: FuncTestCommandQuery: use sort command in PATH.
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+ Thanks to Tomoaki Nishiyama who reports the issue.
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+ (https://github.com/bioruby/bioruby/pull/13)
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+
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+ test/functional/bio/test_command.rb | 6 +++---
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+ 1 files changed, 3 insertions(+), 3 deletions(-)
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+
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+ commit 2f464aae016387cd50031f9d9664e78e220e2d01
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 12 20:37:18 2011 +0900
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+
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+ RELEASE_NOTES.rdoc is updated following recent changes.
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+
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+ RELEASE_NOTES.rdoc | 21 ++++++++++++++-------
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+ 1 files changed, 14 insertions(+), 7 deletions(-)
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+
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+ commit d1a193684afdfd4c632ef75a978d4f3680d1bdf3
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Aug 12 20:30:53 2011 +0900
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+
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+ README.rdoc: changed required Ruby version etc.
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+
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+ * README.rdoc: now Ruby 1.8.6 or later is required.
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+ * README.rdoc: removed old obsolete descriptions.
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+ * README.rdoc: modified about RubyGems.
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+ * KNOWN_ISSUES.rdoc: moved descriptions about older RubyGems and CVS
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+ from README.rdoc.
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+ * KNOWN_ISSUES.rdoc: modified about end-of-life Ruby versions.
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+
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+ KNOWN_ISSUES.rdoc | 40 ++++++++++++++++++++++++++++++----
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+ README.rdoc | 61 ++++++++++++++++++++--------------------------------
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+ 2 files changed, 59 insertions(+), 42 deletions(-)
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+
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+ commit b5cbdc6ab7e81aae4db9aeb708fac57ffbce5636
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat Jul 16 00:12:17 2011 +0900
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+
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+ Added topics for the release notes
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+
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+ RELEASE_NOTES.rdoc | 39 ++++++++++++++++++++++++++++++++++++++-
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+ 1 files changed, 38 insertions(+), 1 deletions(-)
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+
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+ commit f062b5f37a6d8ad35b5b10c942fd61e1a4d37e08
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat Jul 2 01:05:42 2011 +0900
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+
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+ Speedup of Bio::RestrictionEnzyme::Analysis.cut.
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+
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+ * Speedup of Bio::RestrictionEnzyme::Analysis.cut. The new code
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+ is 50 to 80 fold faster than the previous code when cutting
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+ 1Mbp sequence running on Ruby 1.9.2p180.
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+ * Thanks to Tomoaki NISHIYAMA who wrote the first version of the
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+ patch. Thanks to ray1729 (on GitHub) who reports the issue.
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+ (https://github.com/bioruby/bioruby/issues/10)
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+
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+ lib/bio/util/restriction_enzyme.rb | 3 +
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+ .../restriction_enzyme/range/sequence_range.rb | 14 ++--
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+ .../range/sequence_range/calculated_cuts.rb | 75 +++++++++++++++-----
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+ .../range/sequence_range/fragment.rb | 4 +-
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+ 4 files changed, 69 insertions(+), 27 deletions(-)
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+
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+ commit 735379421d9d6b7ceb06b91dcfcca6d5ff841236
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Sat Jul 2 00:59:58 2011 +0900
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+
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+ New classes (for internal use only) for restriction enzyme classes
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+
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+ * New classes Bio::RestrictionEnzyme::SortedNumArray and
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+ Bio::RestrictionEnzyme::DenseIntArray. Both of them are for
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+ Bio::RestrictionEnzyme internal use only. They will be used
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+ for the speedup of restriction enzyme analysis.
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+
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+ lib/bio/util/restriction_enzyme/dense_int_array.rb | 195 ++++++++++++++
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+ .../util/restriction_enzyme/sorted_num_array.rb | 219 +++++++++++++++
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+ .../restriction_enzyme/test_dense_int_array.rb | 201 ++++++++++++++
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+ .../restriction_enzyme/test_sorted_num_array.rb | 281 ++++++++++++++++++++
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+ 4 files changed, 896 insertions(+), 0 deletions(-)
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+ create mode 100644 lib/bio/util/restriction_enzyme/dense_int_array.rb
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+ create mode 100644 lib/bio/util/restriction_enzyme/sorted_num_array.rb
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+ create mode 100644 test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb
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+ create mode 100644 test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb
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+
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+ commit 6cbb0c230d1a0bf3125c3b0fdb9ec3333d9564f8
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Jun 30 20:47:26 2011 +0900
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+
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+ A sample benchmark script for Bio::RestrictionEnzyme::Analysis.cut
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+
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+ sample/test_restriction_enzyme_long.rb | 4403 ++++++++++++++++++++++++++++++++
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+ 1 files changed, 4403 insertions(+), 0 deletions(-)
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+ create mode 100644 sample/test_restriction_enzyme_long.rb
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+
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+ commit 413442bd7424f837c73d8170ced8e01a01f87a59
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue May 24 23:26:41 2011 +0900
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+
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+ Added a test for Bio::FastaFormat#entry_overrun etc.
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+
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+ * Added a test for Bio::FastaFormat#entry_overrun.
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+ * Removed a void test class.
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+
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+ test/unit/bio/db/test_fasta.rb | 24 ++++++++++++------------
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+ 1 files changed, 12 insertions(+), 12 deletions(-)
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+
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+ commit b74020ff9b5c9fc8531c584898a329987008870e
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue May 24 22:21:17 2011 +0900
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+
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+ Bug fix: Bio::FastaFormat#query passes nil to the given factory
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+
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+ * Bug fix: Bio::FastaFormat#query passes nil to the given factory
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+ object. Thanks to Philipp Comans who reports the bug.
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+ (https://github.com/bioruby/bioruby/issues/35)
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+ * Test method for Bio::FastaFormat#query is added.
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+
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+ lib/bio/db/fasta.rb | 2 +-
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+ test/unit/bio/db/test_fasta.rb | 22 ++++++++++++++++++++++
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+ 2 files changed, 23 insertions(+), 1 deletions(-)
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+
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+ commit 80e49373e0e9013442680ba33499be80c58471db
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue May 17 22:33:56 2011 +0900
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+
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+ Changed database name in the example.
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+
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+ * Changed database name in the example.
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+ Thanks to Philipp Comans who reports the issue.
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+
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+ lib/bio/appl/blast.rb | 2 +-
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+ 1 files changed, 1 insertions(+), 1 deletions(-)
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+
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+ commit 7427d1f1355a6c190c6bf8522978e462dea64134
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu May 12 22:15:37 2011 +0900
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+
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+ Bug fix: changed GenomeNet remote BLAST URL.
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+
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+ * Bug fix: changed GenomeNet remote BLAST host name and path.
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+ Thanks to Philipp Comans who reports the bug.
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+ ( https://github.com/bioruby/bioruby/issues/34 )
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+
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+ lib/bio/appl/blast/genomenet.rb | 6 +++---
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+ 1 files changed, 3 insertions(+), 3 deletions(-)
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+
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+ commit c1c231b0a17c06ec042534245ed903e0256a59ed
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue May 10 20:57:17 2011 +0900
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+
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+ updated doc/Tutorial.rd.html
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+
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+ doc/Tutorial.rd.html | 34 ++++++++++++++++++----------------
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+ 1 files changed, 18 insertions(+), 16 deletions(-)
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+
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+ commit 5261c926cae8dac890d7d0380e84f2eb88912417
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+ Author: Pjotr Prins <pjotr.public01@thebird.nl>
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+ Date: Thu May 5 12:07:54 2011 +0200
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+
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+ Tutorial: Fixed URL and the intro
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+
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+ doc/Tutorial.rd | 34 ++++++++++++++++++++--------------
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+ 1 files changed, 20 insertions(+), 14 deletions(-)
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+
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+ commit 71de394053376f4759d705c52e6f16eca3da9d62
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+ Author: Pjotr Prins <pjotr.public01@thebird.nl>
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+ Date: Wed Mar 9 10:26:53 2011 +0100
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+
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+ Tutorial: Added a commnet for rubydoctest, changed Ruby version
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+
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+ * Added a comment for rubydoctest
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+ * Changed example Ruby version representation
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+ * This is part of commit ba5b9c2d29223860252451110a99d4ff0250395d
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+ and modified to merge with the current HEAD.
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+
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+ doc/Tutorial.rd | 4 ++--
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+ 1 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit 1d27153065b8e8595a470b2201961b0a39bf8ca1
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Apr 28 23:58:57 2011 +0900
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+
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+ updated doc/Tutorial.rd.html
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+
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+ doc/Tutorial.rd.html | 2 +-
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+ 1 files changed, 1 insertions(+), 1 deletions(-)
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+
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+ commit ae9beff3bc43db3724a292b10a214583d9fbc111
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Wed Apr 6 11:46:54 2011 -0400
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+
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+ Updated through the section on Homology searching with BLAST
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+
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+ doc/Tutorial.rd | 64 ++++++++++++++++++++--------------------------
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+ doc/Tutorial.rd.html | 68 ++++++++++++++++++++++----------------------------
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+ 2 files changed, 58 insertions(+), 74 deletions(-)
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+
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+ commit 971da799b16628a927abd7dd6c218994506f8fd8
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Thu Mar 24 18:29:20 2011 -0400
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+
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+ Updated the html file generated from the RDoc
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+
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+ doc/Tutorial.rd.html | 224 ++++++++++++++++++++++++++------------------------
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+ 1 files changed, 117 insertions(+), 107 deletions(-)
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+
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+ commit c6afd7eeed121926b56d300cb4170b5024f29eb0
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Thu Mar 24 18:08:17 2011 -0400
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+
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+ Finished updating the tutorial
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+
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+ doc/Tutorial.rd | 16 ++++++++--------
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+ 1 files changed, 8 insertions(+), 8 deletions(-)
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+
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+ commit 7349ac550ec03e2c5266496297becbdb3f4e0edd
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Thu Mar 24 15:56:37 2011 -0400
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+
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+ Edited tutorial up through the extra stuff section
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+
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+ doc/Tutorial.rd | 28 ++++++++++++++--------------
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+ 1 files changed, 14 insertions(+), 14 deletions(-)
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+
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+ commit 32ba3b15ad00d02b12ef2b44636505e23caaf620
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Thu Mar 24 15:26:48 2011 -0400
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+
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+ Updated tutorial up through BioSQL
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+
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+ doc/Tutorial.rd | 172 ++++++++++++++++++-------------------------------------
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+ 1 files changed, 57 insertions(+), 115 deletions(-)
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+
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+ commit 249580edb49a13545708fdcb559104217e37f162
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Thu Mar 24 12:09:03 2011 -0400
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+
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+ Updated tutorial through the section on alignments
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+
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+ doc/Tutorial.rd | 40 +++++++++++++++++++++++++++++++++-------
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+ 1 files changed, 33 insertions(+), 7 deletions(-)
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+
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+ commit 54f7b54044bb245ec5953dc7426f1c434b41f24f
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+ Author: Michael O'Keefe <okeemf@rpi.edu>
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+ Date: Thu Mar 24 11:51:23 2011 -0400
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+
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+ Updated the tutorial (mostly grammar fixes) up until GenBank
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+
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+ doc/Tutorial.rd | 31 +++++++++++++++----------------
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+ 1 files changed, 15 insertions(+), 16 deletions(-)
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+
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+ commit f046a52081a8af0e9afbf65fd2673c29689be769
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue Feb 8 12:58:50 2011 +0900
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+
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+ Added a test protein sequence data for BLAST test.
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+
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+ test/data/fasta/EFTU_BACSU.fasta | 8 ++++++++
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+ 1 files changed, 8 insertions(+), 0 deletions(-)
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+ create mode 100644 test/data/fasta/EFTU_BACSU.fasta
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+
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+ commit f61a5f4bdde16fa051f43cbe3efef4570b415a6a
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+ Author: Anthony Underwood <email2ants@gmail.com>
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+ Date: Mon Jan 31 12:44:55 2011 +0000
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+
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+ Bug fix: GenBank sequence output should format date as 27-JAN-2011
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+
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+ * Bug fix: GenBank sequence output should format date as 27-JAN-2011
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+ rather than 2011-01-27 as specified by offical GenBank specs.
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+
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+ lib/bio/db/genbank/format_genbank.rb | 2 +-
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+ 1 files changed, 1 insertions(+), 1 deletions(-)
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+
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+ commit be144e75a059058ab000a55d7bf535597e7e2617
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Feb 3 20:28:03 2011 +0900
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+
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+ Added tests for remote BLAST execution via GenomeNet and DDBJ.
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+
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+ * Added tests for remote BLAST execution via GenomeNet and DDBJ.
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+ Currently, a test for DDBJ BLAST web API is disabled because
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+ it takes relatively long time.
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+ * Tests to retrieve remote BLAST database information for GenomeNet
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+ and DDBJ servers are also added.
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+
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+ test/functional/bio/appl/blast/test_remote.rb | 93 +++++++++++++++++++++++++
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+ test/functional/bio/appl/test_blast.rb | 61 ++++++++++++++++
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+ 2 files changed, 154 insertions(+), 0 deletions(-)
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+ create mode 100644 test/functional/bio/appl/blast/test_remote.rb
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+ create mode 100644 test/functional/bio/appl/test_blast.rb
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+
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+ commit 67314f1f1a248954c030f7ffe048faf862bf07d2
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Feb 3 20:19:11 2011 +0900
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+
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+ Updated _parse_databases following the changes in the DDBJ server
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+
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+ * Updated _parse_databases following the changes in the DDBJ server.
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+ Changed to use (NT) or (AA) in the tail of each description.
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+ Thanks to DDBJ to improve their web service API.
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+
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+ lib/bio/appl/blast/ddbj.rb | 29 ++++++++++++++++++++---------
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+ 1 files changed, 20 insertions(+), 9 deletions(-)
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+
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+ commit d6aad2f4cc53c1227c86b6b573644cca15c9ed82
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Wed Feb 2 00:02:32 2011 +0900
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+
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+ Release notes for the next release is added.
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+
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+ RELEASE_NOTES.rdoc | 38 ++++++++++++++++++++++++++++++++++++++
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+ 1 files changed, 38 insertions(+), 0 deletions(-)
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+ create mode 100644 RELEASE_NOTES.rdoc
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+
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+ commit b4a30cc8ac9472b9e1c2a298afc624d0229c64c9
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue Feb 1 23:33:18 2011 +0900
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+
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+ Bug fix: Execution failure due to the changes of DDBJ BLAST server
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+
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+ lib/bio/appl/blast/ddbj.rb | 4 +++-
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+ 1 files changed, 3 insertions(+), 1 deletions(-)
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+
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+ commit d30cb5975febd8b526088612c4fb9689a6cc46ba
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue Feb 1 23:01:34 2011 +0900
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+
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+ Support for database "mine-aa" and "mine-nt" with KEGG organism codes
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+
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+ * Added support for database "mine-aa" and "mine-nt" combined with
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+ KEGG organism codes. When database name starts with mine-aa or
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+ mine-nt, space-separated list of KEGG organism codes can be given.
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+ For example, "mine-aa eco bsu hsa".
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+
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+ lib/bio/appl/blast/genomenet.rb | 11 +++++++++++
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+ 1 files changed, 11 insertions(+), 0 deletions(-)
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+
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+ commit abcba798ccf57894dcd570a6578ef78db30a3e25
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue Feb 1 22:20:02 2011 +0900
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+
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+ RELEASE_NOTES.rdoc is renamed to doc/RELEASE_NOTES-1.4.1.rdoc
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+
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+ RELEASE_NOTES.rdoc | 104 ------------------------------------------
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+ doc/RELEASE_NOTES-1.4.1.rdoc | 104 ++++++++++++++++++++++++++++++++++++++++++
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+ 2 files changed, 104 insertions(+), 104 deletions(-)
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+ delete mode 100644 RELEASE_NOTES.rdoc
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+ create mode 100644 doc/RELEASE_NOTES-1.4.1.rdoc
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+
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+ commit 8719cf4e06fc8a8cd0564aeb0b95372a7a0bcefb
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue Feb 1 22:07:32 2011 +0900
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+
565
+ Bug: Options "-v" and "-b" should be used for the limit of hits.
566
+
567
+ * Bug: Options "-v" and "-b" should be used for the limit of hits,
568
+ and "-V" and "-B" should not be used for the purpose.
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+
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+ lib/bio/appl/blast/genomenet.rb | 8 ++++----
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+ 1 files changed, 4 insertions(+), 4 deletions(-)
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+
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+ commit 974b640badae9837fe9fc173d690b27c9b045454
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Tue Feb 1 20:34:50 2011 +0900
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+
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+ Bug fix: Workaround for a change in the GenomeNet BLAST site.
578
+
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+ * Bug fix: Workaround for a change in the GenomeNet BLAST site.
580
+ Thanks to the anonymous reporter. The patch was originally made
581
+ by Toshiaki Katyama.
582
+
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+ lib/bio/appl/blast/genomenet.rb | 7 +++----
584
+ 1 files changed, 3 insertions(+), 4 deletions(-)
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+
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+ commit 001d3e3570c77185cece4aed1be5be2ed6f94f7e
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Thu Jan 6 23:39:19 2011 +0900
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+
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+ Added tests to check the previous Bio::Reference#endnote fix.
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+
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+ test/unit/bio/test_reference.rb | 30 ++++++++++++++++++++++++++++++
593
+ 1 files changed, 30 insertions(+), 0 deletions(-)
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+
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+ commit e1cd766abe24dbcc08a42103127c75ad0ab929aa
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+ Author: Naohisa Goto <ng@bioruby.org>
597
+ Date: Thu Jan 6 23:07:35 2011 +0900
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+
599
+ Bio::Reference#pubmed_url is updated to follow recent NCBI changes.
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+
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+ lib/bio/reference.rb | 5 ++---
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+ test/unit/bio/test_reference.rb | 5 +++++
603
+ 2 files changed, 7 insertions(+), 3 deletions(-)
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+
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+ commit 48024313a7568a38f4291618708541ae1dac312c
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+ Author: Naohisa Goto <ng@bioruby.org>
607
+ Date: Thu Jan 6 22:56:37 2011 +0900
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+
609
+ Bug fix: Bio::Reference#endnote fails when url is not set
610
+
611
+ * Bug fix: Bio::Reference#endnote fails when url is not set.
612
+ Thanks to Warren Kibbe who reports the bug.
613
+ (https://github.com/bioruby/bioruby/issues#issue/15)
614
+
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+ lib/bio/reference.rb | 2 +-
616
+ 1 files changed, 1 insertions(+), 1 deletions(-)
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+
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+ commit 577278a95340abfa32d3e67415d3a10bc74b82c0
619
+ Author: Pjotr Prins <pjotr.public01@thebird.nl>
620
+ Date: Fri Dec 17 12:16:31 2010 +0100
621
+
622
+ Bug fix: In Bio::MEDLINE#reference, doi field should be filled.
623
+
624
+ * Bug fix: In Bio::MEDLINE#reference, doi field should be filled.
625
+ (https://github.com/bioruby/bioruby/issues#issue/29)
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+
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+ lib/bio/db/medline.rb | 1 +
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+ test/unit/bio/db/test_medline.rb | 1 +
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+ 2 files changed, 2 insertions(+), 0 deletions(-)
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+
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+ commit daa20c85681576d3bfbdc8f87580a4b6227b122c
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+ Author: Naohisa Goto <ng@bioruby.org>
633
+ Date: Thu Jan 6 20:25:03 2011 +0900
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+
635
+ Bug fix: Bio::Newick#reparse failure
636
+
637
+ * Bug fix: Bio::Newick#reparse failure.
638
+ Thanks to jdudley who reports the bug.
639
+ (https://github.com/bioruby/bioruby/issues#issue/28)
640
+ * Tests are added to confirm the bug fix.
641
+
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+ lib/bio/db/newick.rb | 4 +++-
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+ test/unit/bio/db/test_newick.rb | 12 ++++++++++++
644
+ 2 files changed, 15 insertions(+), 1 deletions(-)
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+
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+ commit 16117aefdf57ac3ae16b5568f462f7b919ef005f
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+ Author: Naohisa Goto <ng@bioruby.org>
648
+ Date: Thu Jan 6 20:14:18 2011 +0900
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+
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+ Use setup for the preparation of adding more test methods.
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+
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+ test/unit/bio/db/test_newick.rb | 14 ++++++++++----
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+ 1 files changed, 10 insertions(+), 4 deletions(-)
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+
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+ commit e5dc5896a5c6249e2a6cb03d63a3c2ade36b67e7
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+ Author: Naohisa Goto <ng@bioruby.org>
657
+ Date: Fri Nov 19 21:07:13 2010 +0900
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+
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+ Ruby 1.9 support: suppressed warning "mismatched indentations"
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+
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+ test/unit/bio/db/pdb/test_pdb.rb | 4 ++--
662
+ 1 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit 1bce41c7ebed46ac6cf433b047fe6a4c3a538089
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+ Author: Naohisa Goto <ng@bioruby.org>
666
+ Date: Fri Nov 19 21:05:06 2010 +0900
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+
668
+ Ruby 1.9 support: Suppressed warning "shadowing outer local variable"
669
+
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+ lib/bio/db/pdb/residue.rb | 4 ++--
671
+ 1 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit 0f31727769833ccf9d6891ae192da1bc180223e0
674
+ Author: Naohisa Goto <ng@bioruby.org>
675
+ Date: Fri Nov 19 21:04:07 2010 +0900
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+
677
+ Ruby 1.9 support: Suppressed warning "shadowing outer local variable"
678
+
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+ lib/bio/location.rb | 4 ++--
680
+ 1 files changed, 2 insertions(+), 2 deletions(-)
681
+
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+ commit 70c1135b171fcf47dd9dc1bc396d15d1c3acfa62
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+ Author: Naohisa Goto <ng@bioruby.org>
684
+ Date: Fri Nov 19 21:02:57 2010 +0900
685
+
686
+ Ruby 1.9 support: Suppressed warning "shadowing outer local variable"
687
+
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+ lib/bio/db/pdb/pdb.rb | 14 +++++++-------
689
+ 1 files changed, 7 insertions(+), 7 deletions(-)
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+
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+ commit a77e4ab78211a85aa052ca6645a2051a4f3b76d8
692
+ Author: Naohisa Goto <ng@bioruby.org>
693
+ Date: Fri Nov 19 20:42:22 2010 +0900
694
+
695
+ Ruby 1.9 support: use Array#join instead of Array#to_s
696
+
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+ lib/bio/db/pdb/pdb.rb | 4 ++--
698
+ 1 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit 734c2e54613e3ed5efd95e1212feab8f014d5f19
701
+ Author: Naohisa Goto <ng@bioruby.org>
702
+ Date: Fri Nov 19 20:38:11 2010 +0900
703
+
704
+ Changed to use assert_instance_of
705
+
706
+ * Changed to use assert_instance_of(klass, obj) instead of
707
+ assert_equal(klass, obj.class).
708
+
709
+ test/unit/bio/db/pdb/test_pdb.rb | 16 ++++++++--------
710
+ 1 files changed, 8 insertions(+), 8 deletions(-)
711
+
712
+ commit 490286018c8ce314da441c646ea9c5fb3f765c95
713
+ Author: Naohisa Goto <ng@bioruby.org>
714
+ Date: Fri Nov 19 20:24:36 2010 +0900
715
+
716
+ Float::EPSILON was too small for the delta tolerance.
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+
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+ test/unit/bio/db/pdb/test_pdb.rb | 20 ++++++++++----------
719
+ 1 files changed, 10 insertions(+), 10 deletions(-)
720
+
721
+ commit e92d225cadabe63fe23c7c32a4d1d50a371366cc
722
+ Author: Naohisa Goto <ng@bioruby.org>
723
+ Date: Fri Nov 19 20:16:30 2010 +0900
724
+
725
+ Ruby 1.9 support: use assert_in_delta
726
+
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+ test/unit/bio/db/pdb/test_pdb.rb | 24 +++++++++++++++---------
728
+ 1 files changed, 15 insertions(+), 9 deletions(-)
729
+
730
+ commit 41452971a132ef55de3486022962fa2c333b4c85
731
+ Author: Naohisa Goto <ng@bioruby.org>
732
+ Date: Fri Nov 19 13:19:39 2010 +0900
733
+
734
+ Fixed Object#id problem and suppressed warning messages.
735
+
736
+ * Changed not to call nil.id (==4) invoked from chain.id.
737
+ * Suppressed warning message about useless use of a variable.
738
+ * Suppressed waring about conflict of IDs when testing
739
+ addResidue, addLigand and addChain methods.
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+
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+ test/unit/bio/db/pdb/test_pdb.rb | 119 +++++++++++++++++++-------------------
742
+ 1 files changed, 59 insertions(+), 60 deletions(-)
743
+
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+ commit b4af5826f77002933de9d3c2ddfcc5a7cb5629db
745
+ Author: Naohisa Goto <ng@bioruby.org>
746
+ Date: Wed Nov 17 22:26:26 2010 +0900
747
+
748
+ Adjusted copyright line
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+
750
+ test/unit/bio/db/pdb/test_pdb.rb | 4 ++--
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+ 1 files changed, 2 insertions(+), 2 deletions(-)
752
+
753
+ commit 06fd989072b2287a3accbb60684b8a029bfc0ac3
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+ Author: Naohisa Goto <ng@bioruby.org>
755
+ Date: Wed Nov 17 21:54:05 2010 +0900
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+
757
+ A module name is changed to avoid potential name conflict.
758
+
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+ * A module name is changed to avoid potential name conflict.
760
+ * Removed a Shift_JIS character (Zenkaku space) in a comment line.
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+
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+ test/unit/bio/db/pdb/test_pdb.rb | 4 ++--
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+ 1 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit 09007f93abe8c9c5e7561f082b55ca307a7d4a1e
766
+ Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
767
+ Date: Thu Jul 15 21:06:28 2010 +0900
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+
769
+ Added more unit tests for Bio::PDB
770
+
771
+ * Added more unit tests for Bio::PDB.
772
+ * This is part of combinations of the 13 commits:
773
+ * 555f7b49a43e7c35c82cd48b199af96ca93d4179
774
+ * 2b5c87a9ada248597e0517e22191bb4c88be2a42
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+ * a16e24fa35debdcacd11cf36fdf0e60fe82b3684
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+ * e3607c0f7154a4156fd53ed17470aa3628cd2586
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+ * 4e74c9107f09c5eb3fc7fc9ec38d9d773fe89367
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+ * 605fb0a222f70eeaa1e576d31af484a9a6a2ac27
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+ * 2c8b2b5496fee04b886bfcbd11fb99948816cc28
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+ * 202cf2b1b57fbcac215aa135cf6343af6a49d2ef
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+ * f13c070c763c9035451c3639e6e29c9a156947cd
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+ * 843378e608bd1ef27a713d9be2d50f0f56915b0b
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+ * a9078b8a586b66d8026af612d9a5999c6c77de33
784
+ * f0174a8ca3ee136271c51047fce12597d3fbb58c
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+ * 6675fd930718e41ad009f469b8167f81c9b2ad52
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+
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+ test/unit/bio/db/pdb/test_pdb.rb | 3281 +++++++++++++++++++++++++++++++++++++-
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+ 1 files changed, 3276 insertions(+), 5 deletions(-)
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+
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+ commit 2f6a1d29b14d89ac39b408582c9865ad06560ae1
791
+ Author: Naohisa Goto <ng@bioruby.org>
792
+ Date: Sat Nov 6 00:41:21 2010 +0900
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+
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+ Adjusted test data file path, required files and header descriptions.
795
+
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+ test/unit/bio/db/test_litdb.rb | 8 ++++----
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+ 1 files changed, 4 insertions(+), 4 deletions(-)
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+
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+ commit d3394e69c98b3be63c8287af84dc530830fb977a
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+ Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
801
+ Date: Fri Jun 18 17:11:25 2010 +0900
802
+
803
+ added unit test for Bio::LITDB with a sample file
804
+
805
+ test/data/litdb/1717226.litdb | 13 +++++
806
+ test/unit/bio/db/test_litdb.rb | 95 ++++++++++++++++++++++++++++++++++++++++
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+ 2 files changed, 108 insertions(+), 0 deletions(-)
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+ create mode 100644 test/data/litdb/1717226.litdb
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+ create mode 100644 test/unit/bio/db/test_litdb.rb
810
+
811
+ commit cef1d2c824f138fe268d20eaa9ffd85223c85ef9
812
+ Author: Naohisa Goto <ng@bioruby.org>
813
+ Date: Fri Nov 5 23:54:31 2010 +0900
814
+
815
+ Adjusted test data file path, required files and header descriptions.
816
+
817
+ test/unit/bio/db/test_nbrf.rb | 8 ++++----
818
+ 1 files changed, 4 insertions(+), 4 deletions(-)
819
+
820
+ commit e892e7f9b9b4daadeff44c9e479e6f51f02e383e
821
+ Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
822
+ Date: Fri Jun 25 13:20:46 2010 +0900
823
+
824
+ Added unit tests for Bio::NBRF with test data.
825
+
826
+ * Added unit tests for Bio::NBRF with test data.
827
+ * This is part of combinations of the two commits:
828
+ * 53873a82182e072e738da20381dcb2bfd8bc9e96
829
+ (Modified the unit test for Bio::NBRF)
830
+ * 4675cf85aa9c0b4de9f527f9c6bb80804fdaaaa9
831
+ (Modified Bio::TestNBRF and Bio::TestTRANSFAC.)
832
+
833
+ test/data/pir/CRAB_ANAPL.pir | 6 +++
834
+ test/unit/bio/db/test_nbrf.rb | 82 +++++++++++++++++++++++++++++++++++++++++
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+ 2 files changed, 88 insertions(+), 0 deletions(-)
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+ create mode 100644 test/data/pir/CRAB_ANAPL.pir
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+ create mode 100644 test/unit/bio/db/test_nbrf.rb
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+
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+ commit 4922d5151138312d5a09ac60a06419c23978ba3c
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 23:07:13 2010 +0900
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+
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+ Mock class for testing is moved under the test class
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+
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+ * Mock class for testing is moved under the test class, to avoid
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+ potential name conflicts.
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+
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+ test/unit/bio/db/genbank/test_common.rb | 25 ++++++++++++-------------
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+ 1 files changed, 12 insertions(+), 13 deletions(-)
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+
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+ commit 8f630700bc6dd8c183d08291c66c665394873586
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 23:01:32 2010 +0900
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+
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+ Adjusted header descriptions.
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+
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+ test/unit/bio/db/genbank/test_common.rb | 4 ++--
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+ 1 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit ab3d6384ca721fb6004efb5988461eecefad4d6b
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 22:58:21 2010 +0900
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+
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+ Adjusted test data file path and header descriptions.
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+
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+ test/unit/bio/db/genbank/test_genpept.rb | 8 ++++----
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+ 1 files changed, 4 insertions(+), 4 deletions(-)
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+
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+ commit 1d24aecfac9dbc190cdc3eef0956451cc88cfe4f
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Nov 5 22:54:19 2010 +0900
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+
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+ Adjusted test data file path, required files and header descriptions.
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+
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+ test/unit/bio/db/genbank/test_genbank.rb | 12 ++++++++----
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+ 1 files changed, 8 insertions(+), 4 deletions(-)
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+
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+ commit 09275d8661f3d49a7e40be59a086ba33659b2448
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+ Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
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+ Date: Thu Jun 17 22:08:15 2010 +0900
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+
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+ Added unit tests for Bio::GenPept newly.
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+
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+ * Added unit tests for Bio::GenPept newly.
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+ * This is part of the commit 8e46ff42b627791f259033d5a20c1610e32cfa62
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+ (Added unit tests for NBRF and GenPept newly.)
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+
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+ test/data/genbank/CAA35997.gp | 48 ++++++++++++++++++
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+ test/unit/bio/db/genbank/test_genpept.rb | 81 ++++++++++++++++++++++++++++++
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+ 2 files changed, 129 insertions(+), 0 deletions(-)
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+ create mode 100644 test/data/genbank/CAA35997.gp
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+ create mode 100644 test/unit/bio/db/genbank/test_genpept.rb
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+
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+ commit 2cde22cb358a2b7ec8197866fe35a0b46ebf9b00
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+ Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
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+ Date: Thu Jun 24 18:52:37 2010 +0900
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+
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+ Added unit tests for Bio::NCBIDB::Common
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+
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+ * Added unit tests for Bio::NCBIDB::Common.
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+ * This is part of combination of the 4 commits:
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+ * 7da8d557e8ee53da9d93c6fadfd0d8f493977c81
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+ (added test/unit/bio/db/genbank/test_common.rb newly)
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+ * 2b5c87a9ada248597e0517e22191bb4c88be2a42
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+ (Modified a few lines of Bio::NCBIDB::TestCommon,
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+ Bio::TestPDBRecord and Bio::TestPDB)
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+ * 10c043535dd7bf5b9682b4060183f494742c53df
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+ (Modified unit test for Bio::GenBank::Common)
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+ * 0af08fb988e08948a54e33273861b5460b7f6b2d
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+ (Modified the unit test for Bio::GenBank)
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+
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+ test/unit/bio/db/genbank/test_common.rb | 275 +++++++++++++++++++++++++++++++
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+ 1 files changed, 275 insertions(+), 0 deletions(-)
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+ create mode 100644 test/unit/bio/db/genbank/test_common.rb
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+
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+ commit f775d9b7f7deda2e30d4196d4cf507b59936a654
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+ Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
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+ Date: Sat Jun 26 17:54:32 2010 +0900
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+
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+ Added unit tests for Bio::GenBank with test data.
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+
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+ * Added unit tests for Bio::GenBank with test data.
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+ * This is part of combination of the two commits:
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+ * 555f7b49a43e7c35c82cd48b199af96ca93d4179
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+ (added test_genbank.rb and test_go.rb with the test files.
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+ modified test_pdb.rb)
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+ * a46f895bf378ce08143ff031ddda302f970c270a
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+ (Modified Bio::GenBank and Bio::Nexus)
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+
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+ test/data/genbank/SCU49845.gb | 167 +++++++++++++
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+ test/unit/bio/db/genbank/test_genbank.rb | 397 ++++++++++++++++++++++++++++++
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+ 2 files changed, 564 insertions(+), 0 deletions(-)
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+ create mode 100644 test/data/genbank/SCU49845.gb
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+ create mode 100644 test/unit/bio/db/genbank/test_genbank.rb
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+
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+ commit 33621c1f4c16173efd05861759f577b2c4733a53
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Oct 29 16:45:22 2010 +0900
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+
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+ Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".
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+
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+ bioruby.gemspec | 2 +-
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+ lib/bio/version.rb | 2 +-
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+ 2 files changed, 2 insertions(+), 2 deletions(-)
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+
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+ commit cfb2c744f3762689077f5bf2092f715d25e066ed
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+ Author: Naohisa Goto <ng@bioruby.org>
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+ Date: Fri Oct 22 13:02:03 2010 +0900
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+
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+ BioRuby 1.4.1 is released.
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+
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+ ChangeLog | 55 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
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+ 1 files changed, 55 insertions(+), 0 deletions(-)
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+
1
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  commit 92cfda14c08b270ed1beca33153125141f88510e
2
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  Author: Naohisa Goto <ng@bioruby.org>
3
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  Date: Fri Oct 22 13:00:09 2010 +0900