commit 5c88896357e1eff0686ceb06cbec0a7837f85050
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 21:55:41 2009 +0900

    Preparation for bioruby-1.4.0 release.

 lib/bio/version.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 11f56d3d8efc2cf5d9408da865af044fa099b925
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 21:52:25 2009 +0900

    Added about ChangeLog which is replaced by git-log.

 RELEASE_NOTES.rdoc |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

commit 17d5b1825b6c73d710d72903d8710caa9996353a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 20:11:49 2009 +0900

    ChangeLog is autogenerated from git log.
    
     * ChangeLog is autogenerated from git log with the following command:
        % git log --stat --summary \
              3d1dfcc0e13ad582b9c70c7fdde3a89d0bacdc80..HEAD > ChangeLog

 ChangeLog | 2306 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 2306 insertions(+), 0 deletions(-)
 create mode 100644 ChangeLog

commit 02bf77af589ea62df81e9634df6fe949df2fd3ef
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 19:25:39 2009 +0900

    test_output_size is disabled because it depends on html decorations

 test/functional/bio/appl/test_pts1.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 5781fb402e85e73fd47948b4466c8129355b714b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 19:21:21 2009 +0900

    The PTS1 Predictor's URL had been changed.
    
     * The PTS1 Predictor's URL had been changed.
     * Changed to use @uri instead of @host and @cgi_path.

 lib/bio/appl/pts1.rb |    6 ++----
 1 files changed, 2 insertions(+), 4 deletions(-)

commit a4e691d913e1ae51eadb1a871efc2c8718ef5587
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 18:33:00 2009 +0900

    Preparation of ChangeLog autogeneration: old ChangeLog is moved to doc/ChangeLog-before-1.3.1.

 ChangeLog                  | 3961 --------------------------------------------
 doc/ChangeLog-before-1.3.1 | 3961 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 3961 insertions(+), 3961 deletions(-)
 delete mode 100644 ChangeLog
 create mode 100644 doc/ChangeLog-before-1.3.1

commit c011604766baa3cdf5ca2f4a776aa67c56460d29
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 17:53:51 2009 +0900

    Tutorial.rd.html is regenerated.

 doc/Tutorial.rd.html |   70 +++++++++++++------------------------------------
 1 files changed, 19 insertions(+), 51 deletions(-)

commit 6e2cdd13d61970aa4704475bfb5aefb70719c2e1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 17:42:25 2009 +0900

    Added Bio::NCBI.default_email= in the example, and examples using deprecated Bio::PubMed methods are temporarily commented out.

 doc/Tutorial.rd |    8 ++++++++
 1 files changed, 8 insertions(+), 0 deletions(-)

commit 8e6d5e9baf98be7e58f4dda8b5d043a42149874b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 17:15:09 2009 +0900

    Reinserted "==>" for Blast example, and removed duplicated Ruby Ensembl API example.

 doc/Tutorial.rd |   25 ++-----------------------
 1 files changed, 2 insertions(+), 23 deletions(-)

commit 849edd7e8c5b26923cab47e7f5542948fab2b1fb
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sun Dec 27 09:49:14 2009 +0100

    Tutorial: Added info on how to run rubydoctest
              Removed bioruby> prefix for one failing BLAST test

 doc/Tutorial.rd |   69 ++++++++++++++++++++++++++++++++++++++----------------
 1 files changed, 48 insertions(+), 21 deletions(-)

commit a39fcf0ca1a5265789110f42cc616fc5d3c16414
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 25 12:30:18 2009 +0900

    Modified for release notes and fixed typo.

 RELEASE_NOTES.rdoc |   29 +++++++++++++++--------------
 1 files changed, 15 insertions(+), 14 deletions(-)

commit 3fa8b68f19fc2b6aaf8f54eb10517cc761b2193b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 25 12:10:34 2009 +0900

    Changes following the rename to RELEASE_NOTES.rdoc.

 README.rdoc         |    2 +-
 bioruby.gemspec     |    6 +++---
 bioruby.gemspec.erb |    2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

commit fd692a1165d368b9bdbe068ea6bf63fd91c9925c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 25 12:03:41 2009 +0900

    Renamed doc/Changes-1.4.rdoc to RELEASE_NOTES.rdoc.

 RELEASE_NOTES.rdoc   |  160 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/Changes-1.4.rdoc |  160 --------------------------------------------------
 2 files changed, 160 insertions(+), 160 deletions(-)
 create mode 100644 RELEASE_NOTES.rdoc
 delete mode 100644 doc/Changes-1.4.rdoc

commit 0e37f04dd8d34517693fdd4bc27f8bdada7c2f13
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 21:48:52 2009 +0900

    Changed Bio::PhyloXML::Parser.new to open, and regenerated html.

 doc/Tutorial.rd      |   10 ++--
 doc/Tutorial.rd.html |  125 ++++++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 112 insertions(+), 23 deletions(-)

commit aeacbbd425c2e88369c171bd92c60bf8e520a9e5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:26:49 2009 +0900

    bioruby.gemspec is regenerated

 bioruby.gemspec |    8 +++++++-
 1 files changed, 7 insertions(+), 1 deletions(-)

commit 1034205c199a638c359780922293f8b39c467356
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:24:56 2009 +0900

    Version number changed to 1.4.0-rc1

 lib/bio/version.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 04bf2da43f78fbb702b67323f3be1fe3bd2d0351
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:22:41 2009 +0900

    Issues added and modified.

 KNOWN_ISSUES.rdoc |   35 +++++++++++++++++++++++++++++++++--
 1 files changed, 33 insertions(+), 2 deletions(-)

commit f1a76157b009fb0ca94d9a0e0f8a85522c383b19
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:22:19 2009 +0900

    Added news and incompatible changes.

 doc/Changes-1.4.rdoc |  102 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 files changed, 98 insertions(+), 4 deletions(-)

commit 9c8ef18a20c49f17d5b89aa1db5819b2c8ee9b1d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:10:02 2009 +0900

    Email address for NCBI Entrez is given with Bio::NCBI.default_email=.

 bin/bioruby                           |    5 ++++-
 sample/demo_ncbi_rest.rb              |    2 ++
 sample/demo_pubmed.rb                 |    2 ++
 sample/pmfetch.rb                     |    2 ++
 sample/pmsearch.rb                    |    2 ++
 test/functional/bio/io/test_pubmed.rb |    4 ++++
 6 files changed, 16 insertions(+), 1 deletions(-)

commit 7a7179665694da35ab0970909bfbda9ad1b057da
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:09:09 2009 +0900

    Changed autoload hierarchy of Bio::NCBI.

 lib/bio.rb             |   10 ++++++----
 lib/bio/io/ncbisoap.rb |    3 ++-
 2 files changed, 8 insertions(+), 5 deletions(-)

commit f8dc0268d9edf699fd3f0cf18dd55a2b10ec3bcc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 18:58:18 2009 +0900

    New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
    
     * New singleton methods Bio::NCBI.default_email=, default_email,
       default_tools=, default_tools, etc., because email and tool
       parameters will be mandatory in Entrez eUtils.
     * Changed to raise error when email or tool is empty. Note that
       default email is nil and library users should always set their
       email address.
     * Default tool name is changed to include $0 and bioruby version ID.
     * Added multi-thread support for Bio::NCBI::REST#ncbi_access_wait.

 lib/bio/io/ncbirest.rb |  161 ++++++++++++++++++++++++++++++++++++++---------
 1 files changed, 130 insertions(+), 31 deletions(-)

commit 2e311dc44290ef6bda48f0bcba09a3c22bf32d9a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 21 22:24:52 2009 +0900

    Description about the incompatible change of Bio::KEGG::REACTION#rpairs.

 doc/Changes-1.4.rdoc |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit d57ace3a89077caae3c681743da4b92d16b90af8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 21 22:17:46 2009 +0900

    Bio::KEGG::R#ACTION#rpairs is changed to return a hash.

 lib/bio/db/kegg/reaction.rb            |   65 ++++++++++++++++++++++++--------
 test/unit/bio/db/kegg/test_reaction.rb |   27 ++++++++++++-
 2 files changed, 74 insertions(+), 18 deletions(-)

commit 60e4c77d184ee81c51668b446518cfbc9256be50
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 21 22:15:44 2009 +0900

    Document bug fix: return value mistake.

 lib/bio/db/kegg/genes.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 6376dd55aa4995769746e556ca719d37f02975d6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Dec 20 17:32:52 2009 +0900

    Added README.txt for FASTQ example data.

 test/data/fastq/README.txt |  109 ++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 109 insertions(+), 0 deletions(-)
 create mode 100644 test/data/fastq/README.txt

commit 8dec18794c846726733d66c5a22170f5b2c4bb1a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 15 13:51:13 2009 +0900

    Newly added unit tests for Bio::KEGG::GLYCAN with test data.

 test/data/KEGG/G00024.glycan         |   47 ++++++
 test/data/KEGG/G01366.glycan         |   18 +++
 test/unit/bio/db/kegg/test_glycan.rb |  260 ++++++++++++++++++++++++++++++++++
 3 files changed, 325 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/G00024.glycan
 create mode 100644 test/data/KEGG/G01366.glycan
 create mode 100644 test/unit/bio/db/kegg/test_glycan.rb

commit 90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 15 11:42:39 2009 +0900

    Newly added unit test for Bio::KEGG::DRUG with test data.

 test/data/KEGG/D00063.drug         |  104 +++++++++++++++++++
 test/unit/bio/db/kegg/test_drug.rb |  194 ++++++++++++++++++++++++++++++++++++
 2 files changed, 298 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/D00063.drug
 create mode 100644 test/unit/bio/db/kegg/test_drug.rb

commit 443f778795b82a7f572cb8b85d2a8a8b3cea1334
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 15 11:38:59 2009 +0900

    New method Bio::KEGG::DRUG#products
    
     * New method Bio::KEGG::DRUG#products.
     * Improved RDoc.

 lib/bio/db/kegg/drug.rb |   50 +++++++++++++++++++++++++++++++++++++---------
 1 files changed, 40 insertions(+), 10 deletions(-)

commit 48184d96b989f909ac0effb759cbc4b1ddc98dd1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:36:54 2009 +0900

    Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables.

 lib/bio/db/kegg/common.rb |   62 ++++++++++++++++++++++++++------------------
 1 files changed, 37 insertions(+), 25 deletions(-)

commit f364ea609f1e01ca5270a5bd7404e0bbf752bc89
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:23:42 2009 +0900

    Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.

 bioruby.gemspec     |  142 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 bioruby.gemspec.erb |    4 +-
 lib/bio/version.rb  |    4 +-
 3 files changed, 145 insertions(+), 5 deletions(-)

commit 096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:22:59 2009 +0900

    Added documents about Bio::KEGG incompatible changes.

 doc/Changes-1.4.rdoc |   48 ++++++++++++++++++++++++++++++++++++++++++------
 1 files changed, 42 insertions(+), 6 deletions(-)

commit 72ed277fe30bb1033cbc16d462f137510afb84e6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:21:26 2009 +0900

    Newly added unit tests for Bio::KEGG::ENZYME with test data.

 test/data/KEGG/1.1.1.1.enzyme        |  935 ++++++++++++++++++++++++++++++++++
 test/unit/bio/db/kegg/test_enzyme.rb |  241 +++++++++
 2 files changed, 1176 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/1.1.1.1.enzyme
 create mode 100644 test/unit/bio/db/kegg/test_enzyme.rb

commit b99fcb39f7c5d2857cbb65283d85ea868ae8561d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:09:03 2009 +0900

    Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
    
     * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the
       method dblinks is changed to return a Hash. The old methods  are
       renamed to dblinks_as_strings.
     * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION,
       the method  pathways is changed to return a Hash. The old methods
       are renamed to pathways_as_strings except for GENES.
     * In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method
       orthologs is changed to return a Hash. The old methods are renamed
       to orthologs_as_strings.
     * Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed
       to return a Hash. The old methods are renamed to genes_as_strings.
     * Added Bio::KEGG::REACTION#rpairs_as_tokens, older behavior of rpairs.
     * Modules in lib/bio/db/kegg/common.rb are moved uner Bio::KEGG::Common
       namespace.
     * Refactoring.
     * Added documents.
     * Tests modified.

 lib/bio/db/kegg/common.rb              |   40 +++++++++++++++++++++++++------
 lib/bio/db/kegg/compound.rb            |   10 ++++---
 lib/bio/db/kegg/drug.rb                |   27 +++++++++++++++------
 lib/bio/db/kegg/enzyme.rb              |   31 ++++++++++++++++++++----
 lib/bio/db/kegg/genes.rb               |   39 +++++++++++++++++++------------
 lib/bio/db/kegg/glycan.rb              |   22 +++++++++++++++--
 lib/bio/db/kegg/orthology.rb           |   25 +++++++------------
 lib/bio/db/kegg/reaction.rb            |   16 +++++++++---
 test/unit/bio/db/kegg/test_compound.rb |   27 ++++++++++++--------
 test/unit/bio/db/kegg/test_reaction.rb |   13 +++++----
 10 files changed, 170 insertions(+), 80 deletions(-)

commit 2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 10 16:02:54 2009 +0900

    Bio::KEGG::GENES#structure no more adds PDB: prefix.
    
     * Bio::KEGG::GENES#structure no more adds PDB: prefix.
     * Added Bio::KEGG::GENES#structures as an alias of structure.

 lib/bio/db/kegg/genes.rb            |    7 +++----
 test/unit/bio/db/kegg/test_genes.rb |    7 ++++---
 2 files changed, 7 insertions(+), 7 deletions(-)

commit a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 10 15:28:33 2009 +0900

    Refactoring of Bio::KEGG::Orthology#dblinks and genes.
    
     * Refactoring of Bio::KEGG::Orthology#dblinks and genes: no need
       to treat @data because lines_fetch internally does so.

 lib/bio/db/kegg/orthology.rb |   10 ++--------
 1 files changed, 2 insertions(+), 8 deletions(-)

commit 720e0bccdfdc6fac6222cac1a9f05d6e2419896c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 9 16:39:03 2009 +0900

    Changed dummy lines for RDoc.

 lib/bio/db/kegg/compound.rb  |    4 ++--
 lib/bio/db/kegg/orthology.rb |    2 +-
 lib/bio/db/kegg/reaction.rb  |    4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

commit 20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 9 15:17:39 2009 +0900

    Refactoring of Bio::KEGG::REACTION#orthologs.
    
     * Refactoring of Bio::KEGG::REACTION#orthologs: no need to treat
       @data because lines_fetch internally does so.

 lib/bio/db/kegg/reaction.rb |    5 +----
 1 files changed, 1 insertions(+), 4 deletions(-)

commit b924601bacd643f66b37dd991913e6862df704a9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Dec 6 15:51:03 2009 +0900

    Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.
    
     * Bio::KEGG::GENES#pathways is changed to return raw lines as an
       Array of strings.
     * RDoc is added for Bio::KEGG::GENES.

 lib/bio/db/kegg/genes.rb |   99 ++++++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 96 insertions(+), 3 deletions(-)

commit 4c840dc6a539db1d854b23991269b3e6515f637e
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Wed Dec 2 17:02:00 2009 +0900

    Added test methods.

 test/unit/bio/db/kegg/test_compound.rb |   47 ++++++++++++++++++++++++++++++++
 1 files changed, 47 insertions(+), 0 deletions(-)

commit 105efa1ecd1bc99a54aac32710a97df15035119d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 23:31:07 2009 +0900

    Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.

 lib/bio/db/kegg/orthology.rb |   16 +++++-----------
 1 files changed, 5 insertions(+), 11 deletions(-)

commit c394ead051c3a13ceb534f93816af7ad35be932a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 23:07:23 2009 +0900

    Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
    
     * Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash
       with changing its return value to a hash.
     * The code of the orthologs_as_hash method is moved to
       lib/bio/db/kegg/common.rb.
     * Added new method Bio::KEGG::REACTION#orthologs, copied from
       lib/bio/db/kegg/glycan.rb.

 lib/bio/db/kegg/common.rb              |   18 +++++++++++++++++-
 lib/bio/db/kegg/reaction.rb            |   14 ++++++--------
 sample/demo_kegg_reaction.rb           |    6 ++++--
 test/unit/bio/db/kegg/test_reaction.rb |   12 ++++++++++--
 4 files changed, 37 insertions(+), 13 deletions(-)

commit 4e01fda27166faf066104ab9897904fd46f57123
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 22:48:06 2009 +0900

    Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
    
     * New method Bio::KEGG::REACTION#pathways_as_hash, using a module
       in lib/bio/db/kegg/common.rb.
     * Bio::KEGG::REACTION#pathways is reverted to return an array of
       string.

 lib/bio/db/kegg/reaction.rb            |   18 +++++++++++-------
 test/unit/bio/db/kegg/test_reaction.rb |    8 +++++++-
 2 files changed, 18 insertions(+), 8 deletions(-)

commit 0c2ce4b8462792d496ab3f58206fdbd47143e280
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 22:35:21 2009 +0900

    New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.

 lib/bio/db/kegg/compound.rb            |   14 +++++++++++
 test/unit/bio/db/kegg/test_compound.rb |   38 ++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 0 deletions(-)

commit 63df07e030120eb43de22555277529822b072270
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 22:25:20 2009 +0900

    Methods commonly used from Bio::KEGG::* classes.
    
     * Modules containing methods commonly used from Bio::KEGG::* classes.
       The "dblinks_as_hash" method is copied from
       lib/bio/db/kegg/orthology.rb. The "pathways_as_hash" method is
       derived from the dblinks_as_hash and Bio::KEGG::REACTION#pathways
       methods.

 lib/bio/db/kegg/common.rb |   60 +++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 60 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/kegg/common.rb

commit 0e55c6701b09a52356ac55300181ee656773826f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 21:39:06 2009 +0900

    Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.

 lib/bio/db/kegg/compound.rb            |   11 ++---------
 test/unit/bio/db/kegg/test_compound.rb |    8 +++++++-
 2 files changed, 9 insertions(+), 10 deletions(-)

commit a05adcddf6c7ed67c042f31ecd86848af1ba8a22
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 21:13:39 2009 +0900

    Bug fix: fixed a copy-and-paste mistake.

 lib/bio/db/kegg/drug.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 86925f3c80730e3ea3377a23a70cadb3876258c4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 1 21:31:40 2009 +0900

    Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.

 doc/Changes-1.4.rdoc                    |    4 ++++
 lib/bio/db/kegg/orthology.rb            |    2 +-
 test/unit/bio/db/kegg/test_orthology.rb |    2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

commit 60847cd2d0701fa38a499578649cb216c93993a2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 1 20:41:51 2009 +0900

    Test class names are changed to avoid potential class name conflict.

 test/unit/bio/db/kegg/test_compound.rb  |    2 +-
 test/unit/bio/db/kegg/test_genes.rb     |    4 ++--
 test/unit/bio/db/kegg/test_orthology.rb |    2 +-
 test/unit/bio/db/kegg/test_reaction.rb  |    2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

commit 2bda62af7a020c22379dd9ec3a42496d2a5b94cb
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Tue Dec 1 04:38:27 2009 +0900

    Added unit tests for Bio::KEGG::ORTHOLOGY.

 test/data/KEGG/K02338.orthology         |  902 +++++++++++++++++++++++++++++++
 test/unit/bio/db/kegg/test_orthology.rb |   50 ++
 2 files changed, 952 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/K02338.orthology
 create mode 100644 test/unit/bio/db/kegg/test_orthology.rb

commit acad9497caf5d737394568e911691fdad11ca091
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 30 21:39:32 2009 +0900

    Changed to use BioRubyTestDataPath instead of __FILE__.

 test/unit/bio/db/kegg/test_compound.rb |    3 +--
 test/unit/bio/db/kegg/test_reaction.rb |    3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

commit 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 16:37:21 2009 +0900

    Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
    
     * Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
     * Changes of filenames due to the previous file move.

 lib/bio/db/fasta/format_qual.rb              |   18 ++++++++--------
 lib/bio/db/fastq.rb                          |    7 ++---
 lib/bio/sequence.rb                          |    3 +-
 lib/bio/sequence/quality_score.rb            |   25 +++++++++++------------
 test/unit/bio/sequence/test_quality_score.rb |   28 +++++++++++++-------------
 5 files changed, 40 insertions(+), 41 deletions(-)

commit 2b29654c1d7e927e445e7acdd525835a873c2a2a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 16:15:42 2009 +0900

    lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/. The unit test is also moved.
    
     * lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/.
     * test/unit/bio/db/fastq/test_quality_score.rb is moved to
       test/unit/bio/sequence/.
     * The file contents will be modified with the following commit.

 lib/bio/db/fastq/quality_score.rb            |  206 ----------------
 lib/bio/sequence/quality_score.rb            |  206 ++++++++++++++++
 test/unit/bio/db/fastq/test_quality_score.rb |  330 --------------------------
 test/unit/bio/sequence/test_quality_score.rb |  330 ++++++++++++++++++++++++++
 4 files changed, 536 insertions(+), 536 deletions(-)
 delete mode 100644 lib/bio/db/fastq/quality_score.rb
 create mode 100644 lib/bio/sequence/quality_score.rb
 delete mode 100644 test/unit/bio/db/fastq/test_quality_score.rb
 create mode 100644 test/unit/bio/sequence/test_quality_score.rb

commit aa8d49bf31f90dd2796c18ee0aa6291979284ec2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 15:20:36 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_gff1.rb.

 lib/bio/db/gff.rb   |   17 -----------------
 sample/demo_gff1.rb |   49 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 17 deletions(-)
 create mode 100644 sample/demo_gff1.rb

commit 76fffd2d2429346478fb3d8c88cdcd878a1047b1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 15:06:41 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_tmhmm_report.rb.

 lib/bio/appl/tmhmm/report.rb |   36 ----------------------
 sample/demo_tmhmm_report.rb  |   68 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 36 deletions(-)
 create mode 100644 sample/demo_tmhmm_report.rb

commit dfafb0a2bcec4c0b4cd3640374e151e2039056dc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:59:27 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_targetp_report.rb.

 lib/bio/appl/targetp/report.rb |  105 +------------------------------
 sample/demo_targetp_report.rb  |  135 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 136 insertions(+), 104 deletions(-)
 create mode 100644 sample/demo_targetp_report.rb

commit 75f7c8527546f8ea3079f53b90a9b4d8260b4de0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:33:28 2009 +0900

    Follow-up of the SOSUI server URL change.

 lib/bio/appl/sosui/report.rb |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

commit 8022696295dc296462f73b40cc74ad5259bee387
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:32:11 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sosui_report.rb.

 lib/bio/appl/sosui/report.rb |   53 +------------------------
 sample/demo_sosui_report.rb  |   89 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 90 insertions(+), 52 deletions(-)
 create mode 100644 sample/demo_sosui_report.rb

commit 4acfe7f565039b34a036682912a75f55da808b45
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:02:32 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_hmmer_report.rb.

 lib/bio/appl/hmmer/report.rb |  100 ----------------------------
 sample/demo_hmmer_report.rb  |  149 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 149 insertions(+), 100 deletions(-)
 create mode 100644 sample/demo_hmmer_report.rb

commit 4f7bd1b7628d90661d8b557ca854b14cc44fb99c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 15:49:21 2009 +0900

    Demo codes in the "if __FILE__ == $0" are removed because they are very short.

 lib/bio/appl/fasta/format10.rb |   14 --------------
 lib/bio/appl/hmmer.rb          |   16 +---------------
 lib/bio/io/flatfile.rb         |    8 +-------
 3 files changed, 2 insertions(+), 36 deletions(-)

commit c2a72d195189755532e7e206af34d152ab6332d8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 15:20:28 2009 +0900

    Bug fix: Failure of Bio::Fasta.remote due to the remote site changes.

 lib/bio/appl/fasta.rb |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

commit 549112fb4dfb5f6b2fe3491fb161887a9f5262ac
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 15:13:10 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_fasta_remote.rb.

 lib/bio/appl/fasta.rb       |   18 ---------------
 sample/demo_fasta_remote.rb |   51 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 18 deletions(-)
 create mode 100644 sample/demo_fasta_remote.rb

commit 0e4ca0db83692fdbbe93e90272a07bcbac89192c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 10:17:47 2009 +0900

    Text indents for some comment lines are changed.

 sample/demo_blast_report.rb  |    4 ++--
 sample/demo_kegg_compound.rb |    4 ++--
 sample/demo_prosite.rb       |    4 ++--
 sample/demo_sirna.rb         |    4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

commit c0cf91fe2a9247bc3705b20515f9d4fa14288d5a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 10:13:26 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_keggapi.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_keggapi.rb.
     * Commented out demonstrations of deprecated methods:
       get_neighbors_by_gene, get_similarity_between_genes,
       get_ko_members, get_oc_members_by_gene, get_pc_members_by_gene.
     * Commented out demonstrations of methods internally using
       the deprecated methods: get_all_neighbors_by_gene,
       get_all_oc_members_by_gene, get_all_pc_members_by_gene.

 lib/bio/io/keggapi.rb  |  442 ------------------------------------------
 sample/demo_keggapi.rb |  502 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 502 insertions(+), 442 deletions(-)
 create mode 100644 sample/demo_keggapi.rb

commit 8b8206c1d8ee699185fdd19d3329311c85ee003c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:50:06 2009 +0900

    Fixed the license line.

 lib/bio/db/prosite.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ebfeec8243abd4e2f65335fda1ead18efff66897
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:41:58 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ncbi_rest.rb.

 lib/bio/io/ncbirest.rb   |  101 ------------------------------------
 sample/demo_ncbi_rest.rb |  128 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 128 insertions(+), 101 deletions(-)
 create mode 100644 sample/demo_ncbi_rest.rb

commit 5a0f8379a374650d12fc88fbbd5b28c38ae96395
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:33:07 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_prosite.rb.

 lib/bio/db/prosite.rb  |   95 +-------------------------------------
 sample/demo_prosite.rb |  120 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 121 insertions(+), 94 deletions(-)
 create mode 100644 sample/demo_prosite.rb

commit c560a5d0ba9d4919dbcca156ea620056dcb8f725
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:14:37 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort.rb.

 lib/bio/appl/psort.rb |  111 ---------------------------------------
 sample/demo_psort.rb  |  138 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 138 insertions(+), 111 deletions(-)
 create mode 100644 sample/demo_psort.rb

commit 1299a55d214784a536ae3cd8bfabdfd61fe1da86
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:04:29 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort_report.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_psort_report.rb, without any checks.

 lib/bio/appl/psort/report.rb |   46 +---------------------------
 sample/demo_psort_report.rb  |   70 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+), 45 deletions(-)
 create mode 100644 sample/demo_psort_report.rb

commit a2686fe3c5a93947c94d4602514a62a808c182d5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 00:53:54 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genscan_report.rb.

 lib/bio/appl/genscan/report.rb |  176 ----------------------------------
 sample/demo_genscan_report.rb  |  202 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 202 insertions(+), 176 deletions(-)
 create mode 100644 sample/demo_genscan_report.rb

commit 22f662ba69dd2d4a2273562dd7ea921f5cdd84bd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 00:28:01 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ddbjxml.rb.

 lib/bio/io/ddbjxml.rb  |  182 +-----------------------------------------
 sample/demo_ddbjxml.rb |  212 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 213 insertions(+), 181 deletions(-)
 create mode 100644 sample/demo_ddbjxml.rb

commit ed3b34b6598f632c7b9b3f1a17b42406c19ca32d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 00:12:33 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pubmed.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_pubmed.rb.
     * Codes using Entrez CGI are disabled in the demo.

 lib/bio/io/pubmed.rb  |   88 -------------------------------------
 sample/demo_pubmed.rb |  116 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 116 insertions(+), 88 deletions(-)
 create mode 100644 sample/demo_pubmed.rb

commit 9e6d720f383e88e247eacab6f0e43f38140a62f2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 23:59:10 2009 +0900

    Demo codes in the "if __FILE__ == $0" are removed.
    
     * Demo codes in the "if __FILE__ == $0" are removed because their
       function have already been moved to sample/demo_blast_report.rb.

 lib/bio/appl/blast/format0.rb |  193 --------------------------------------
 lib/bio/appl/blast/report.rb  |  149 +-----------------------------
 lib/bio/appl/blast/wublast.rb |  208 -----------------------------------------
 3 files changed, 2 insertions(+), 548 deletions(-)

commit bbba2812fa9131d01fc655eb174d84f06facd8b8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 23:49:36 2009 +0900

    New demo code of BLAST parser based on codes in "if __FILE__ ==$0"
    
     * Newly added sample/demo_blast_report.rb, demonstration of
       BLAST parsers  Bio::Blast::Report, Bio::Blast::Default::Report,
       and Bio::Blast::WU::Report. It is based on the demonstration codes
       in the "if __FILE__ == $0" in lib/bio/appl/blast/report.rb,
       lib/bio/appl/blast/format0.rb, and lib/bio/appl/blast/wublast.rb.

 sample/demo_blast_report.rb |  285 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 285 insertions(+), 0 deletions(-)
 create mode 100644 sample/demo_blast_report.rb

commit 5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 21:57:08 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_das.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_das.rb.
     * Demo codes using UCSC DAS server is added.
     * Demo using the WormBase DAS server is temporarily disabled because
       it does not work well possibly because of the server trouble.

 lib/bio/io/das.rb  |   44 ----------------------
 sample/demo_das.rb |  105 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+), 44 deletions(-)
 create mode 100644 sample/demo_das.rb

commit b7b0f7bef0505b9678673e54bb863d4ff7897dd5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 20:58:35 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_taxonomy.rb, although it does not work correctly now.

 lib/bio/db/kegg/taxonomy.rb  |   53 +-----------------------
 sample/demo_kegg_taxonomy.rb |   92 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+), 52 deletions(-)
 create mode 100644 sample/demo_kegg_taxonomy.rb

commit 23da98ca19fce1f0b487e1f955ef4cd896839590
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 20:11:12 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_reaction.rb.

 lib/bio/db/kegg/reaction.rb  |   16 +----------
 sample/demo_kegg_reaction.rb |   64 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 15 deletions(-)
 create mode 100644 sample/demo_kegg_reaction.rb

commit 9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 19:12:00 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_orthology.rb.

 lib/bio/db/kegg/orthology.rb  |   23 +--------------
 sample/demo_kegg_orthology.rb |   62 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 22 deletions(-)
 create mode 100644 sample/demo_kegg_orthology.rb

commit 6f6f1eb3d87dea588ea333708c4d4486ac7136b6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 12:19:26 2009 +0900

    Commented out demo for nonexistent method "bindings".

 sample/demo_kegg_glycan.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 98a6d904058b5af4808f16bcb710d73bd97c9764
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 12:18:31 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_glycan.rb.

 lib/bio/db/kegg/glycan.rb  |   21 -------------
 sample/demo_kegg_glycan.rb |   72 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+), 21 deletions(-)
 create mode 100644 sample/demo_kegg_glycan.rb

commit d26e835ca9def2287f1050f1b048892e3cafdaa0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 11:49:05 2009 +0900

    Added references.

 lib/bio/db/kegg/genome.rb |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit c3c460462481b5b8d6e9441216bcf6370b4890ef
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 11:45:31 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_genome.rb.

 lib/bio/db/kegg/genome.rb  |   42 +------------------------
 sample/demo_kegg_genome.rb |   74 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+), 41 deletions(-)
 create mode 100644 sample/demo_kegg_genome.rb

commit 0d8e709b66bf18ead5944c27a50eb6cf2c47862f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 11:43:24 2009 +0900

    Added document about downloading sample data.

 sample/demo_kegg_drug.rb |   13 ++++++++++++-
 1 files changed, 12 insertions(+), 1 deletions(-)

commit 0608893198e9bc88521b6c013069d8c7a13bb0e5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 00:10:48 2009 +0900

    Added documents.

 lib/bio/db/kegg/drug.rb |   15 +++++++++++++++
 1 files changed, 15 insertions(+), 0 deletions(-)

commit 0ecdc1ee0460f16dba1e4cd5ab575c92e1c6b1ac
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 00:06:02 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_drug.rb.

 lib/bio/db/kegg/drug.rb  |   18 +--------------
 sample/demo_kegg_drug.rb |   54 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+), 17 deletions(-)
 create mode 100644 sample/demo_kegg_drug.rb

commit b0c349103f01a26f4741999bd696bf5b1c032e06
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 23:51:13 2009 +0900

    Added documents.

 lib/bio/db/kegg/compound.rb |   10 ++++++++++
 1 files changed, 10 insertions(+), 0 deletions(-)

commit e965b454c553ed9670bc83962a2a9d7c5de49929
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 23:45:15 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_compound.rb.

 lib/bio/db/kegg/compound.rb  |   19 +-------------
 sample/demo_kegg_compound.rb |   57 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+), 18 deletions(-)
 create mode 100644 sample/demo_kegg_compound.rb

commit 7454db7c8b8ef7202736d311356d4ca350af336f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 23:06:21 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_litdb.rb.

 lib/bio/db/litdb.rb  |   17 +----------------
 sample/demo_litdb.rb |   42 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 16 deletions(-)
 create mode 100644 sample/demo_litdb.rb

commit fde284248e013e44184ee2ba7da85e5b83155a69
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 22:57:01 2009 +0900

    Ruby 1.9 support: String#each_line instead of String#each

 lib/bio/db/go.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 8b60099615790fe372b4fde27a391dedc767aab2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 22:53:12 2009 +0900

    Sample code bug fix: fixed method names, and workaround for Zlib error.
    
     * Sample code bug fix: Following method name changes.
     * Workaround for Zlib::DataError.

 sample/demo_go.rb |   13 +++++++++----
 1 files changed, 9 insertions(+), 4 deletions(-)

commit 737fec3db555811d127d2356e5ceef63b0413fb8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:47:14 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_go.rb.

 lib/bio/db/go.rb  |   70 +---------------------------------------
 sample/demo_go.rb |   93 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+), 69 deletions(-)
 create mode 100644 sample/demo_go.rb

commit 8264b15690132d9e766f16d0829bb12cd122b900
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:20:52 2009 +0900

    Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq in the RDoc.
    
     * Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq
       in the RDoc.
     * Modified copyright line.

 lib/bio/appl/bl2seq/report.rb |   18 +++++++++---------
 1 files changed, 9 insertions(+), 9 deletions(-)

commit c572ff022fee43505355608f0a0e3ba2181e87e2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:17:04 2009 +0900

    Bug fix: Failed to read Bio::Blast::Bl2seq::Report data by using Bio::FlatFile.

 lib/bio/appl/bl2seq/report.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 4f6b080623442dfcc5864e2aefde7e53ace068e8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:15:11 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_bl2seq_report.rb.

 lib/bio/appl/bl2seq/report.rb |  194 +------------------------------------
 sample/demo_bl2seq_report.rb  |  220 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 221 insertions(+), 193 deletions(-)
 create mode 100644 sample/demo_bl2seq_report.rb

commit 2f03e8757383e0d1a26c0f6942c74a30f3b26d90
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 18:24:43 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genbank.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_genbank.rb, and modified as below.
        * To get sequences from the NCBI web service.
        * By default, arguments are sequence IDs (accession numbers).
        * New option "--files" (or "-files", "--file", or "-file") to
          read sequences from file(s).

 lib/bio/db/genbank/genbank.rb |   87 +--------------------------
 sample/demo_genbank.rb        |  132 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 133 insertions(+), 86 deletions(-)
 create mode 100644 sample/demo_genbank.rb

commit a2981c28fdb629a655c71c920f6588f8b80aff06
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 15:06:50 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aaindex.rb.

 lib/bio/db/aaindex.rb  |   39 +---------------------------
 sample/demo_aaindex.rb |   67 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 38 deletions(-)
 create mode 100644 sample/demo_aaindex.rb

commit b741d17ec5c5ac234bab35b8716fee072635de1a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 12:45:43 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sirna.rb
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_sirna.rb, and modified for reading normal sequence
       files instead of a raw sequence.

 lib/bio/util/sirna.rb |   24 +------------------
 sample/demo_sirna.rb  |   63 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+), 23 deletions(-)
 create mode 100644 sample/demo_sirna.rb

commit 7cc778e78bc63ef73796ee15d6f0db8d6967aefe
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 23:00:42 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pathway.rb.

 lib/bio/pathway.rb     |  171 -----------------------------------------
 sample/demo_pathway.rb |  196 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 196 insertions(+), 171 deletions(-)
 create mode 100644 sample/demo_pathway.rb

commit 7e5510587abc0b50b6851f005a3236bf9dc79d08
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 22:49:13 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_locations.rb.

 lib/bio/location.rb      |   73 ----------------------------------
 sample/demo_locations.rb |   99 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 99 insertions(+), 73 deletions(-)
 create mode 100644 sample/demo_locations.rb

commit f1c02666f4b11d5cf208d6beb592d8ac962ce2da
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 22:35:50 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_codontable.rb.

 lib/bio/data/codontable.rb |   96 +-----------------------------------
 sample/demo_codontable.rb  |  119 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 120 insertions(+), 95 deletions(-)
 create mode 100644 sample/demo_codontable.rb

commit c11a7793f85faf3d66d630833c38358ffa34a698
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 16:35:16 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_nucleicacid.rb.

 lib/bio/data/na.rb         |   27 +-----------------------
 sample/demo_nucleicacid.rb |   49 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+), 26 deletions(-)
 create mode 100644 sample/demo_nucleicacid.rb

commit de41b67c3f65baa0f122689b2e9f479d8a247934
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 16:25:05 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aminoacid.rb.

 lib/bio/data/aa.rb       |   78 +-----------------------------------
 sample/demo_aminoacid.rb |  101 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 102 insertions(+), 77 deletions(-)
 create mode 100644 sample/demo_aminoacid.rb

commit e652dd44ecb6b6dad652e33a398f92bb8373e7dd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 16:12:48 2009 +0900

    Added an error message about encoding in Ruby 1.9.1

 KNOWN_ISSUES.rdoc |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

commit 003133b0d4e2234c27927c9d10b75185c354102e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 15:52:21 2009 +0900

    changed recommended Ruby version

 README.rdoc |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 408483d36b713678361cecf6c77ff7a2098f71fc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 22 17:07:37 2009 +0900

    added information about doc/Changes-1.4.rdoc

 README.rdoc |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit ef342933839e8c6cef9883045fcaf468aff5da23
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 22 16:50:55 2009 +0900

    In PhyloXML support, added a link to GNOME Libxml2 and fixed RDoc syntax.

 README.rdoc |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

commit 0237ef42d60c7a76cadf8ea78f4251bcfe89c95f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 19 09:43:15 2009 +0900

    Ruby 1.9 support: String#each_line instead of String#each

 lib/bio/appl/meme/mast/report.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ec935ea9b19415bf3325bcc0763fbc22f3c71a3d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 19 09:40:49 2009 +0900

    The "libpath magic" is replaced by loading helper routine.

 test/unit/bio/appl/meme/mast/test_report.rb |   11 ++++++-----
 test/unit/bio/appl/meme/test_mast.rb        |   11 ++++++-----
 test/unit/bio/appl/meme/test_motif.rb       |    8 +++++---
 3 files changed, 17 insertions(+), 13 deletions(-)

commit 3f65eeb503f3b2ef866cab4c73d2d700ca572835
Author: Adam Kraut <adamnkraut@gmail.com>
Date:   Tue Mar 17 19:41:31 2009 -0400

    Added basic support for MEME/MAST applications

 lib/bio/appl/meme/mast.rb                   |  156 +++++++++++++++++++++++++++
 lib/bio/appl/meme/mast/report.rb            |   91 ++++++++++++++++
 lib/bio/appl/meme/motif.rb                  |   48 ++++++++
 test/data/meme/mast.out                     |   13 +++
 test/data/meme/meme.out                     |    3 +
 test/unit/bio/appl/meme/mast/test_report.rb |   45 ++++++++
 test/unit/bio/appl/meme/test_mast.rb        |  102 +++++++++++++++++
 test/unit/bio/appl/meme/test_motif.rb       |   36 ++++++
 8 files changed, 494 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/appl/meme/mast.rb
 create mode 100644 lib/bio/appl/meme/mast/report.rb
 create mode 100644 lib/bio/appl/meme/motif.rb
 create mode 100644 test/data/meme/db
 create mode 100644 test/data/meme/mast
 create mode 100644 test/data/meme/mast.out
 create mode 100644 test/data/meme/meme.out
 create mode 100644 test/unit/bio/appl/meme/mast/test_report.rb
 create mode 100644 test/unit/bio/appl/meme/test_mast.rb
 create mode 100644 test/unit/bio/appl/meme/test_motif.rb

commit 3862f54fda0caec2a07e563a1f8a11913baca2e3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 18 20:29:56 2009 +0900

    New version of PhyloXML schema, version 1.10.
    
     * Upgraded to New version of PhyloXML schema, version 1.10,
       developed by Christian M Zmasek.

 lib/bio/db/phyloxml/phyloxml.xsd | 1155 +++++++++++++++++++-------------------
 1 files changed, 582 insertions(+), 573 deletions(-)

commit 45ffd9228d513b3dbf29e1011c6a6689a8bd1b08
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 18 00:26:44 2009 +0900

    Newly added sample script to test big PhyloXML data
    
     * Newly added a sample script to test big PhyloXML data based on
       Diana Jaunzeikare's work.
       (http://github.com/latvianlinuxgirl/bioruby/blob/
       20627fc5a443d6c2e3dc73ed50e9c578ffcbc330/
       test/unit/bio/db/test_phyloxml_big.rb).

 sample/test_phyloxml_big.rb |  205 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 205 insertions(+), 0 deletions(-)
 create mode 100644 sample/test_phyloxml_big.rb

commit 828a8971e057919b80508cf29fd9518828b74a2f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 17 23:54:37 2009 +0900

    Speed up of Bio::Tree#children and parent: caching node's parent.
    
     * For speed up of Bio::Tree#children and parent, internal cache of
       the parent for each node is added. The cache is automatically
       cleared when the tree is modified. Note that the cache can only
       be accessed from inside Bio::Tree.
     * Bio::Tree#parent is changed to directly raise IndexError when
       both of the root specified in the argument and preset in the
       tree are nil (previously, the same error is raised in the path
       method which is internally called from the parent method).
     * Bio::Tree#path is changed not to call bfs_shortest_path if the
       node1 and node2 are adjacent.

 lib/bio/tree.rb |   75 +++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 files changed, 70 insertions(+), 5 deletions(-)

commit 75862212e6bb807a570338e39e19d527219b6f13
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 22:11:15 2009 +0900

    Documented incompatible changes of Bio::KEGG::COMPOUND and Bio::KEGG:REACTION.

 doc/Changes-1.4.rdoc |   10 ++++++++++
 1 files changed, 10 insertions(+), 0 deletions(-)

commit c74cfabd6414c8b50db0251739f967accd90773f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 21:20:42 2009 +0900

    Ruby compatibility issue: Enumerable#each_slice(4).each does not work in Ruby 1.8.5.

 lib/bio/db/kegg/reaction.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit e6a920e401a2b06c355174ccdc9b993a38f9d7ec
Author: Mitsuteru Nakao <mitsuteru.nakao@gmail.com>
Date:   Wed Jul 22 22:50:22 2009 +0900

    Added new method Bio::KEGG::GENES#structure with the unit tests.

 lib/bio/db/kegg/genes.rb            |   12 ++++++++++++
 test/unit/bio/db/kegg/test_genes.rb |   25 +++++++++++++++++++++++++
 2 files changed, 37 insertions(+), 0 deletions(-)

commit 9fee0c133d069348857014410983f682e468c1c7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 21:04:02 2009 +0900

    The "libpath magic" is replaced by loading helper routine.

 test/unit/bio/db/kegg/test_compound.rb |    6 ++++--
 test/unit/bio/db/kegg/test_reaction.rb |    6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

commit 1199330eab95b8434303e92c5f792818e96db814
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Sat Nov 14 09:03:50 2009 +0900

    Newly added unit tests for Bio::KEGG::COMPOUND and Bio::KEGG::REACTION
    
     * Newly added unit tests for Bio::KEGG::COMPOUND and
       Bio::KEGG::REACTION with test data. (Note that this is a
       combination of several commits made by Kozo Nishida,
       merged from git://github.com/kozo2/bioruby.git ).

 test/data/KEGG/C00025.compound         |  102 ++++++++++++++++++++++++++++++++
 test/data/KEGG/R00006.reaction         |   14 ++++
 test/unit/bio/db/kegg/test_compound.rb |   49 +++++++++++++++
 test/unit/bio/db/kegg/test_reaction.rb |   57 ++++++++++++++++++
 4 files changed, 222 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/C00025.compound
 create mode 100644 test/data/KEGG/R00006.reaction
 create mode 100644 test/unit/bio/db/kegg/test_compound.rb
 create mode 100644 test/unit/bio/db/kegg/test_reaction.rb

commit 1b47640665d4332bafd9e9709628ee9722f1f3f4
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Sat Nov 14 09:03:50 2009 +0900

    Bio::KEGG::COMPOUND#dblinks changed to return hash list
    
     * Bio::KEGG::COMPOUND#dblinks is changed to return hash list (array
       containing hashes).

 lib/bio/db/kegg/compound.rb |   11 +++++++++--
 1 files changed, 9 insertions(+), 2 deletions(-)

commit 2aa43a0aa765ee4502923c2102e352826a9a7abd
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Sat Nov 14 07:29:19 2009 +0900

    Bio::KEGG:REACTION#rpair and pathways changed to return hash list, and added orthologies method.
    
     * New method: Bio::KEGG:REACTION#orthologies
     * Bio::KEGG:REACTION#rpair and pathways are changed to return hash
       list (array containing hashes).

 lib/bio/db/kegg/reaction.rb |   33 ++++++++++++++++++++++++++++++---
 1 files changed, 30 insertions(+), 3 deletions(-)

commit a82f5d228370beeeb397be07e07394652fd7837e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 20:03:19 2009 +0900

    Changed not to modify given argument

 lib/bio/util/restriction_enzyme/single_strand.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ff10d5540759a5e7eaaa71da020d95170b98e007
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 19:50:08 2009 +0900

    Newly added a document for incompatible and/or important changes of the new release version.
    
     * Newly added a document for incompatible and/or important changes
       of the new release version.
     * Added description about Bio::RestrictionEnzyme validation is
       disabled (although very small change).

 doc/Changes-1.4.rdoc |   16 ++++++++++++++++
 1 files changed, 16 insertions(+), 0 deletions(-)
 create mode 100644 doc/Changes-1.4.rdoc

commit 629e537f90e0825fadeec2e0207f8caddfbed59a
Author: trevor <>
Date:   Sat Sep 19 11:03:23 2009 -0500

    speed-up serial calls to RestrictionEnzyme

 lib/bio/db/rebase.rb                               |    2 +-
 lib/bio/util/restriction_enzyme/single_strand.rb   |    3 +-
 .../util/restriction_enzyme/test_single_strand.rb  |   24 ++++++++++---------
 .../test_single_strand_complement.rb               |   24 ++++++++++---------
 4 files changed, 29 insertions(+), 24 deletions(-)

commit 9b55a92d5300294bef7b624d0f9aa3edd3e8d7fc
Author: trevor <>
Date:   Sat Sep 19 10:46:21 2009 -0500

    speed-up rebase library

 lib/bio/db/rebase.rb |    9 ++++-----
 1 files changed, 4 insertions(+), 5 deletions(-)

commit 4aaa24b3fc3cf2d1f7cf8b6d974d2115958b5a1b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 15:08:31 2009 +0900

    Ruby 1.9 support: Array#to_s is changed to join('')

 lib/bio/db/sanger_chromatogram/scf.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 1cf924b81150545e807169144aeaca6a75f9731c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 12:59:10 2009 +0900

    Ruby 1.9 support: Array#nitems (counts the number of non-nil elements) is removed in 1.9.
    
     * Ruby 1.9 support: Array#nitems (counts the number of non-nil
       elements) is removed in Ruby 1.9. In scf.rb, it seems that
       nil would never be included in the array, and simply replaced
       by Array#size.

 lib/bio/db/sanger_chromatogram/scf.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit a95994d9cfbf4fc89fa716358ac5b92d42a1307b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 15 19:23:12 2009 +0900

    Bug fix: error when quality_scores are larger than the sequence length, and added a require line.
    
     * Bug fix: error when sequence.quality_scores are larger than
       the sequence length.
     * Added a require line.

 lib/bio/db/fasta/format_qual.rb |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

commit c5aafca19b58b1651080e81699b7020cd3fd3f47
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 15 19:21:49 2009 +0900

    Newly added unit tests for Bio::Sequence::Format::Formatter::Fasta_numeric and Qual.

 test/unit/bio/db/fasta/test_format_qual.rb |  346 ++++++++++++++++++++++++++++
 1 files changed, 346 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/db/fasta/test_format_qual.rb

commit 6e24170e29d2576ff69b18eaadc94e9769b8612a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Nov 14 02:41:13 2009 +0900

    Newly added Bio::Sequence::Format::Formatter::Qual and Fasta_numeric, formatter for Qual format and FastaNumericFormat.

 lib/bio/db/fasta/format_qual.rb |  201 +++++++++++++++++++++++++++++++++++++++
 lib/bio/sequence/format.rb      |    7 ++
 2 files changed, 208 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/fasta/format_qual.rb

commit 6959fd359040b6ca9570111d515118dc2d472029
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Nov 14 02:19:17 2009 +0900

    Split quality score methods in Bio::Fastq::FormatData into separete modules
    
     * Quality score calculation methods in Bio::Fastq::FormatData in
       lib/bio/db/fastq.rb is splitted into separate modules
       Bio::Fastq::QualityScore::Converter, Phred, and Solexa
       in lib/bio/db/fastq/quality_score.rb.
     * Unit tests for Bio::Fastq::QualityScore::* are newly added
       in test/unit/bio/db/fastq/test_quality_score.rb.
     * Possible bug fix: probability should be 0 <= p <= 1.

 lib/bio/db/fastq.rb                          |  112 +--------
 lib/bio/db/fastq/quality_score.rb            |  206 ++++++++++++++++
 test/unit/bio/db/fastq/test_quality_score.rb |  330 ++++++++++++++++++++++++++
 3 files changed, 544 insertions(+), 104 deletions(-)
 create mode 100644 lib/bio/db/fastq/quality_score.rb
 create mode 100644 test/unit/bio/db/fastq/test_quality_score.rb

commit 98f7703c28f0c2c34e4fe1631de227e20b9666c3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 23:48:19 2009 +0900

    When no error_probabilities in the sequence and quality_score_type is nil, Fastq formatter implicitly assumes that the quality_score_type is :phred.
    
     * When no error_probabilities in the sequence and
       quality_score_type is nil, Fastq formatter implicitly assumes
       that the quality_score_type is :phred.
     * Bug fix: fixed typo in lib/bio/db/fastq/format_fastq.rb.

 lib/bio/db/fastq/format_fastq.rb |    5 ++++-
 lib/bio/sequence.rb              |    3 +++
 2 files changed, 7 insertions(+), 1 deletions(-)

commit f85a6aee9827bc573dcb735f4a1a1827926cc66c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 23:29:19 2009 +0900

    Bug fix: fixed typo for Bio::Sequence#quality_score_type.

 lib/bio/sequence.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit d81a611d7c7c46a789b86e99cebe064ba559e3e0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 20:42:12 2009 +0900

    Splitting lib/bio/db/fasta.rb: FastaNumericFormat is moved to a new file, etc.
    
     * Splitting lib/bio/db/fasta.rb as follows:
        * Bio::FastaNumericFormat is moved to lib/bio/db/fasta/qual.rb.
        * Demo codes in the "if __FILE__ == $0" are moved to
          sample/demo_fastaformat.rb.
     * Unit tests for Bio::FastaNumericFormat are moved from
       test/unit/bio/db/test_fasta.rb to test/unit/bio/db/test_qual.rb.
     * lib/bio.rb is also modified for the autoload.
     * Bug fix: fixed incorrect autoload path for Bio::FastaDefline.

 lib/bio.rb                     |    4 +-
 lib/bio/db/fasta.rb            |  135 +---------------------------------------
 lib/bio/db/fasta/qual.rb       |  102 ++++++++++++++++++++++++++++++
 sample/demo_fastaformat.rb     |  105 +++++++++++++++++++++++++++++++
 test/unit/bio/db/test_fasta.rb |   43 -------------
 test/unit/bio/db/test_qual.rb  |   63 +++++++++++++++++++
 6 files changed, 273 insertions(+), 179 deletions(-)
 create mode 100644 lib/bio/db/fasta/qual.rb
 create mode 100644 sample/demo_fastaformat.rb
 create mode 100644 test/unit/bio/db/test_qual.rb

commit c70bed5c3f828c94084fdeabe255fbb3930097d0
Author: Andrew Grimm <andrew.j.grimm@gmail.com>
Date:   Sun Aug 16 19:49:38 2009 +1000

    Removed use of uninitialized variable in FastaNumericFormat.

 lib/bio/db/fasta.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ce6dcc344a3d7beec544d7164308dd97bafa8a19
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 13:04:11 2009 +0900

    User data type should be stored as is, even if unknown data type.

 lib/bio/db/sanger_chromatogram/abif.rb |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

commit ca96e59f151c2e10b5cd8c0690b8297979e52036
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 12:50:59 2009 +0900

    Removed Bio::Abif#method_missing and added alternative method
    
     * Removed Bio::Abif#method_missing, because method_missing can
       hide many errors related to method calls e.g. method name typo,
       and it is not suitable for only getting data.
     * New method Bio::Abif#data is added to get data (alternative of
       the method_missing).

 lib/bio/db/sanger_chromatogram/abif.rb |   19 ++++++++++++-------
 1 files changed, 12 insertions(+), 7 deletions(-)

commit 8b0da27523998cb9a9df07f5e907cda6e3cef0dc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 12:04:41 2009 +0900

    removed a non-ascii character in comment

 lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 55c1a180fec97338bae8e3c5b5d5ceec64aed0f6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 12:02:53 2009 +0900

    Bug fix: Bio::SangerChromatogram#complement fails when the object is frozen.

 lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 4e7d8b0ba304d1ff01364fad68035f7ec9463fb9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 12 22:23:47 2009 +0900

    fixed a typo in a copyright line

 test/unit/bio/util/test_sirna.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit f376124112d23ba9b0491dbd427d328edc81d872
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 12 22:05:37 2009 +0900

    The "libpath magic" in tests are replaced by the load of helper routine.
    
     * In all unit tests, the "libpath magic" are replaced by the load
       of helper routine.
     * Changed to use a constant BioRubyTestDataPath for generating test
       data file path.
     * Some "require" lines are modified.
     * "File.open(...).read" in some tests are replaced by "File.read(...)".
     * Header comment lines of some tests with wrong filename and/or
       class/module name information are fixed.

 test/functional/bio/appl/test_pts1.rb              |    6 ++++--
 test/functional/bio/io/test_ensembl.rb             |    7 ++++---
 test/functional/bio/io/test_pubmed.rb              |    8 +++++---
 test/functional/bio/io/test_soapwsdl.rb            |    9 +++++----
 test/functional/bio/io/test_togows.rb              |    9 +++++----
 test/functional/bio/sequence/test_output_embl.rb   |   10 ++++++----
 test/functional/bio/test_command.rb                |   10 +++++-----
 test/runner.rb                                     |    8 +++++---
 test/unit/bio/appl/bl2seq/test_report.rb           |    9 +++++----
 test/unit/bio/appl/blast/test_ncbioptions.rb       |    6 ++++--
 test/unit/bio/appl/blast/test_report.rb            |    9 +++++----
 test/unit/bio/appl/blast/test_rpsblast.rb          |    9 +++++----
 test/unit/bio/appl/gcg/test_msf.rb                 |   10 +++++-----
 test/unit/bio/appl/genscan/test_report.rb          |   17 ++++++++---------
 test/unit/bio/appl/hmmer/test_report.rb            |    9 +++++----
 test/unit/bio/appl/iprscan/test_report.rb          |   11 ++++++-----
 test/unit/bio/appl/mafft/test_report.rb            |   11 ++++++-----
 test/unit/bio/appl/paml/codeml/test_rates.rb       |    9 +++++----
 test/unit/bio/appl/paml/codeml/test_report.rb      |    9 +++++----
 test/unit/bio/appl/paml/test_codeml.rb             |    9 +++++----
 test/unit/bio/appl/sim4/test_report.rb             |    9 +++++----
 test/unit/bio/appl/sosui/test_report.rb            |   11 ++++++-----
 test/unit/bio/appl/targetp/test_report.rb          |    8 +++++---
 test/unit/bio/appl/test_blast.rb                   |    9 +++++----
 test/unit/bio/appl/test_fasta.rb                   |    6 ++++--
 test/unit/bio/appl/test_pts1.rb                    |    6 ++++--
 test/unit/bio/appl/tmhmm/test_report.rb            |   11 ++++++-----
 test/unit/bio/data/test_aa.rb                      |    8 +++++---
 test/unit/bio/data/test_codontable.rb              |    9 +++++----
 test/unit/bio/data/test_na.rb                      |    8 +++++---
 test/unit/bio/db/biosql/tc_biosql.rb               |    6 +++++-
 test/unit/bio/db/embl/test_common.rb               |    6 ++++--
 test/unit/bio/db/embl/test_embl.rb                 |   12 ++++++------
 test/unit/bio/db/embl/test_embl_rel89.rb           |   12 ++++++------
 test/unit/bio/db/embl/test_embl_to_bioseq.rb       |   15 +++++++--------
 test/unit/bio/db/embl/test_sptr.rb                 |   14 ++++++--------
 test/unit/bio/db/embl/test_uniprot.rb              |   11 ++++++-----
 test/unit/bio/db/kegg/test_genes.rb                |    8 +++++---
 test/unit/bio/db/pdb/test_pdb.rb                   |    6 ++++--
 test/unit/bio/db/sanger_chromatogram/test_abif.rb  |    3 ++-
 test/unit/bio/db/sanger_chromatogram/test_scf.rb   |    3 ++-
 test/unit/bio/db/test_aaindex.rb                   |   12 ++++++------
 test/unit/bio/db/test_fasta.rb                     |    8 +++++---
 test/unit/bio/db/test_fastq.rb                     |   10 +++++-----
 test/unit/bio/db/test_gff.rb                       |    6 ++++--
 test/unit/bio/db/test_lasergene.rb                 |   12 +++++++-----
 test/unit/bio/db/test_medline.rb                   |    6 ++++--
 test/unit/bio/db/test_newick.rb                    |   12 ++++++------
 test/unit/bio/db/test_nexus.rb                     |    6 ++++--
 test/unit/bio/db/test_phyloxml.rb                  |   14 +++++++-------
 test/unit/bio/db/test_phyloxml_writer.rb           |   15 +++++++--------
 test/unit/bio/db/test_prosite.rb                   |   11 ++++++-----
 test/unit/bio/db/test_rebase.rb                    |    8 +++++---
 test/unit/bio/db/test_soft.rb                      |   13 +++++++------
 test/unit/bio/io/flatfile/test_autodetection.rb    |   13 ++++++-------
 test/unit/bio/io/flatfile/test_buffer.rb           |   11 ++++++-----
 test/unit/bio/io/flatfile/test_splitter.rb         |    8 ++++----
 test/unit/bio/io/test_ddbjxml.rb                   |    7 ++++---
 test/unit/bio/io/test_ensembl.rb                   |    8 +++++---
 test/unit/bio/io/test_fastacmd.rb                  |    7 ++++---
 test/unit/bio/io/test_flatfile.rb                  |   11 ++++++-----
 test/unit/bio/io/test_soapwsdl.rb                  |    7 ++++---
 test/unit/bio/io/test_togows.rb                    |    6 ++++--
 test/unit/bio/sequence/test_aa.rb                  |    8 +++++---
 test/unit/bio/sequence/test_common.rb              |    6 ++++--
 test/unit/bio/sequence/test_compat.rb              |    6 ++++--
 test/unit/bio/sequence/test_dblink.rb              |    8 +++++---
 test/unit/bio/sequence/test_na.rb                  |    6 ++++--
 test/unit/bio/shell/plugin/test_seq.rb             |    8 +++++---
 test/unit/bio/test_alignment.rb                    |    8 +++++---
 test/unit/bio/test_command.rb                      |    7 ++++---
 test/unit/bio/test_db.rb                           |    8 +++++---
 test/unit/bio/test_feature.rb                      |    6 ++++--
 test/unit/bio/test_location.rb                     |    6 ++++--
 test/unit/bio/test_map.rb                          |    8 +++++---
 test/unit/bio/test_pathway.rb                      |    6 ++++--
 test/unit/bio/test_reference.rb                    |    6 ++++--
 test/unit/bio/test_sequence.rb                     |    8 +++++---
 test/unit/bio/test_shell.rb                        |    8 +++++---
 test/unit/bio/test_tree.rb                         |   12 ++++++------
 .../analysis/test_calculated_cuts.rb               |    6 ++++--
 .../restriction_enzyme/analysis/test_cut_ranges.rb |    6 ++++--
 .../analysis/test_sequence_range.rb                |    6 ++++--
 .../double_stranded/test_aligned_strands.rb        |    6 ++++--
 .../double_stranded/test_cut_location_pair.rb      |    6 ++++--
 .../test_cut_location_pair_in_enzyme_notation.rb   |    6 ++++--
 .../double_stranded/test_cut_locations.rb          |    6 ++++--
 .../test_cut_locations_in_enzyme_notation.rb       |    6 ++++--
 .../test_cut_locations_in_enzyme_notation.rb       |    6 ++++--
 .../bio/util/restriction_enzyme/test_analysis.rb   |    6 ++++--
 .../bio/util/restriction_enzyme/test_cut_symbol.rb |    6 ++++--
 .../restriction_enzyme/test_double_stranded.rb     |    6 ++++--
 .../util/restriction_enzyme/test_single_strand.rb  |    6 ++++--
 .../test_single_strand_complement.rb               |    6 ++++--
 .../restriction_enzyme/test_string_formatting.rb   |    6 ++++--
 test/unit/bio/util/test_color_scheme.rb            |    8 +++++---
 test/unit/bio/util/test_contingency_table.rb       |    8 +++++---
 test/unit/bio/util/test_restriction_enzyme.rb      |    6 ++++--
 test/unit/bio/util/test_sirna.rb                   |    8 +++++---
 99 files changed, 479 insertions(+), 343 deletions(-)

commit f4fa0a5edc6ff6fc35577d84bda86363014a57a4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 11 17:04:43 2009 +0900

    test_chromatogram.rb is splitted into test_abif.rb and test_scf.rb

 test/unit/bio/db/sanger_chromatogram/test_abif.rb  |   75 +++++++++++++++
 .../db/sanger_chromatogram/test_chromatogram.rb    |  101 --------------------
 test/unit/bio/db/sanger_chromatogram/test_scf.rb   |   97 +++++++++++++++++++
 3 files changed, 172 insertions(+), 101 deletions(-)
 create mode 100644 test/unit/bio/db/sanger_chromatogram/test_abif.rb
 delete mode 100644 test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
 create mode 100644 test/unit/bio/db/sanger_chromatogram/test_scf.rb

commit d9cc613273cadc7f9fdfe2bafbd933efb1f403ca
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 11 17:01:37 2009 +0900

    Newly added unit test helper routine which aims to replace the libpath magic

 test/bioruby_test_helper.rb |   61 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 61 insertions(+), 0 deletions(-)
 create mode 100644 test/bioruby_test_helper.rb

commit 10e76db2a8ec37bde541157d0735303b4ca8b3b8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 10 20:59:01 2009 +0900

    Bio::SangerChromatogram#to_s is renamed to sequence_string.

 lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 0ec2c2f38c4b4a3e451841dc32540dfa10743bc2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 30 22:49:19 2009 +0900

    Renamed/moved files/directories following the rename of class names.
    
     * renamed: lib/bio/db/chromatogram.rb ->
                lib/bio/db/sanger_chromatogram/chromatogram.rb
     * renamed: lib/bio/db/chromatogram/abi.rb ->
                lib/bio/db/sanger_chromatogram/abif.rb
     * renamed: lib/bio/db/chromatogram/scf.rb ->
                lib/bio/db/sanger_chromatogram/scf.rb
     * renamed: lib/bio/db/chromatogram/chromatogram_to_biosequence.rb ->
                lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
     * renamed: test/unit/bio/db/test_chromatogram.rb ->
                test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
     * renamed: test/data/chromatogram/test_chromatogram_abi.ab1 ->
                test/data/sanger_chromatogram/test_chromatogram_abif.ab1
     * renamed: test/data/chromatogram/*.scf ->
                test/data/sanger_chromatogram/*.scf

 lib/bio/db/chromatogram.rb                         |  133 -------------
 lib/bio/db/chromatogram/abi.rb                     |  114 -----------
 .../db/chromatogram/chromatogram_to_biosequence.rb |   32 ---
 lib/bio/db/chromatogram/scf.rb                     |  210 --------------------
 lib/bio/db/sanger_chromatogram/abif.rb             |  114 +++++++++++
 lib/bio/db/sanger_chromatogram/chromatogram.rb     |  133 +++++++++++++
 .../chromatogram_to_biosequence.rb                 |   32 +++
 lib/bio/db/sanger_chromatogram/scf.rb              |  210 ++++++++++++++++++++
 test/data/chromatogram/test_chromatogram_abi.ab1   |  Bin 228656 -> 0 bytes
 .../data/chromatogram/test_chromatogram_scf_v2.scf |  Bin 47503 -> 0 bytes
 .../data/chromatogram/test_chromatogram_scf_v3.scf |  Bin 47503 -> 0 bytes
 .../sanger_chromatogram/test_chromatogram_abif.ab1 |  Bin 0 -> 228656 bytes
 .../test_chromatogram_scf_v2.scf                   |  Bin 0 -> 47503 bytes
 .../test_chromatogram_scf_v3.scf                   |  Bin 0 -> 47503 bytes
 .../db/sanger_chromatogram/test_chromatogram.rb    |  101 ++++++++++
 test/unit/bio/db/test_chromatogram.rb              |  101 ----------
 16 files changed, 590 insertions(+), 590 deletions(-)
 delete mode 100644 lib/bio/db/chromatogram.rb
 delete mode 100644 lib/bio/db/chromatogram/abi.rb
 delete mode 100644 lib/bio/db/chromatogram/chromatogram_to_biosequence.rb
 delete mode 100644 lib/bio/db/chromatogram/scf.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/abif.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/chromatogram.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/scf.rb
 delete mode 100644 test/data/chromatogram/test_chromatogram_abi.ab1
 delete mode 100644 test/data/chromatogram/test_chromatogram_scf_v2.scf
 delete mode 100644 test/data/chromatogram/test_chromatogram_scf_v3.scf
 create mode 100644 test/data/sanger_chromatogram/test_chromatogram_abif.ab1
 create mode 100644 test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf
 create mode 100644 test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf
 create mode 100644 test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
 delete mode 100644 test/unit/bio/db/test_chromatogram.rb

commit 49bfe319e535c8414be32b47c07fe5204a24b398
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 30 22:02:08 2009 +0900

    Renamed Chromatogram to SangerChromatogram and Abi to Abif, and preparation of filename changes.
    
     * Renamed Chromatogram to SangerChromatogram because the word
       "chromatogram" may be used by various experimental methods
       other than the Sanger chromatogram.
     * Renamed Abi to Abif because Applied Biosystems who determined
       the file format says that its name is ABIF.
     * Preparation of changing filenames. However, filenames are
       not really changed now because of recording history of file
       contents modification. The paths shown in the "require" lines
       and test data paths may not be existed now.

 lib/bio.rb                                         |    6 ++--
 lib/bio/db/chromatogram.rb                         |   24 +++++++-------
 lib/bio/db/chromatogram/abi.rb                     |   15 +++++----
 .../db/chromatogram/chromatogram_to_biosequence.rb |   10 +++---
 lib/bio/db/chromatogram/scf.rb                     |   15 +++++----
 lib/bio/sequence/adapter.rb                        |    3 +-
 test/unit/bio/db/test_chromatogram.rb              |   32 ++++++++++---------
 7 files changed, 57 insertions(+), 48 deletions(-)

commit 6c020440663214014973ae8e5007ce2d31d8d45e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 24 00:44:47 2009 +0900

    New class method Bio::PhyloXML::Parser.open(filename) and API change of new(), etc.
    
     * New class methods to create parser object from various data
       source are added: Bio::PhyloXML::Parser.open(filename),
       for_io(io), open_uri(uri).
     * API change of Bio::PhyloXML::Parser.new(). Now, new(filename)
       is deprecated and it can only take a XML-formatted string.
     * Tests are added and modified to reflect the above changes.
     * test/unit/bio/db/test_phyloxml_writer.rb: avoid using WeakRef
       for temporary directory maintenance.

 lib/bio/db/phyloxml/phyloxml_parser.rb   |  224 +++++++++++++++++++++++++++---
 lib/bio/db/phyloxml/phyloxml_writer.rb   |    4 +-
 test/unit/bio/db/test_phyloxml.rb        |  178 ++++++++++++++++++++++--
 test/unit/bio/db/test_phyloxml_writer.rb |   70 +++++-----
 4 files changed, 408 insertions(+), 68 deletions(-)

commit fca5e800fc051a38ac6d25652c684fdd4f9bff14
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 23 15:13:25 2009 +0900

    Rearrangement of require and autoload so as to correctly load PhyloXML classes

 lib/bio.rb                               |   11 +++++++----
 lib/bio/db/phyloxml/phyloxml_elements.rb |   16 +++++++++++++++-
 lib/bio/db/phyloxml/phyloxml_parser.rb   |   11 ++++++-----
 lib/bio/db/phyloxml/phyloxml_writer.rb   |    5 ++++-
 test/unit/bio/db/test_phyloxml.rb        |    5 -----
 test/unit/bio/db/test_phyloxml_writer.rb |    3 ---
 6 files changed, 32 insertions(+), 19 deletions(-)

commit a291af62ef262ee04f3a0e1b6415d4e256c56a94
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 23 00:08:44 2009 +0900

    Fixed argument order of assert_equal(expected, actual), etc.
    
     * Test bug fix: Argument order of assert_equal must be
       assert_equal(expected, actual).
     * assert_instance_of() instead of assert_equal() in
       TestPhyloXML1#test_init.
     * Removed some commented-out tests which may not be needed.

 test/unit/bio/db/test_phyloxml.rb        |  295 +++++++++++++++---------------
 test/unit/bio/db/test_phyloxml_writer.rb |    8 +-
 2 files changed, 147 insertions(+), 156 deletions(-)

commit 152304dc9809102f56a2f1779c59111f84b9cd02
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:40:49 2009 +0900

    Improvement of tests for Bio::Fastq and related classes.

 test/unit/bio/db/test_fastq.rb |  372 ++++++++++++++++++++++++++--------------
 1 files changed, 245 insertions(+), 127 deletions(-)

commit 61556223a469a5f8b1bb4f343eca92c88c66cb9a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:38:52 2009 +0900

    FASTQ output support is added to Bio::Sequence.

 lib/bio/db/fastq/format_fastq.rb |  172 ++++++++++++++++++++++++++++++++++++++
 lib/bio/sequence/format.rb       |    9 ++
 2 files changed, 181 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/fastq/format_fastq.rb

commit ea4203ebb7ca268a5b6d6c50aeb63ed0eed5a803
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:32:50 2009 +0900

    New attributes for genome sequencer data are added to Bio::Sequence.
    
     * New attributes for genome sequencer data are added to
       Bio::Sequence class: quality_scores, quality_scores_type,
       error_probabilities.

 lib/bio/sequence.rb |   13 +++++++++++++
 1 files changed, 13 insertions(+), 0 deletions(-)

commit fce158b2194519081361e12c170882ec2e87fc5e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:13:27 2009 +0900

    New methods Bio::Fastq#to_biosequence, etc. and improvement of tolerance for overflows
    
     * Bio::Fastq#to_biosequence is newly added.
     * New methods: Bio::Fastq#seq, entry_id, quality_score_type.
     * Default behavior of Bio::Fastq::FormatData#scores2str is changed
       not to raise error but to truncate saturated values.
     * Improvement of tolerance for overflows, and preventing to calculate
       log of negative number.

 lib/bio/db/fastq.rb                      |  105 ++++++++++++++++++++++++++++--
 lib/bio/db/fastq/fastq_to_biosequence.rb |   40 +++++++++++
 lib/bio/sequence/adapter.rb              |    1 +
 3 files changed, 139 insertions(+), 7 deletions(-)
 create mode 100644 lib/bio/db/fastq/fastq_to_biosequence.rb

commit 0f189974d2027cecee575b27e969de7f62508309
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Oct 13 21:41:58 2009 +0900

    Avoid using Numeric#fdiv because it can only be used in Ruby 1.8.7 or later

 lib/bio/db/fastq.rb            |    6 +++---
 test/unit/bio/db/test_fastq.rb |   10 +++++-----
 2 files changed, 8 insertions(+), 8 deletions(-)

commit 42999fc6230e52c4f241f411d299db941196f62e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Oct 13 21:30:25 2009 +0900

    Bio::Fastq#qualities is renamed to quality_scores.
    
     * Bio::Fastq#qualities is renamed to Bio::Fastq#quality_scores, and
       the original method name is changed to be an alias of the new name.

 lib/bio/db/fastq.rb            |   16 +++++++++-------
 test/unit/bio/db/test_fastq.rb |   30 +++++++++++++++---------------
 2 files changed, 24 insertions(+), 22 deletions(-)

commit cc0ee2169f298046c5e55fcbadfeaac01f6bf704
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Oct 11 19:19:18 2009 +0900

    Newly added unit tests for Bio::Fastq with test data
    
     * Newly added unit tests for Bio::Fastq with test data. The test data
       is created by P.J.A. Cock et al., and is also used in Biopython and
       BioPerl.

 test/data/fastq/error_diff_ids.fastq               |   20 +
 test/data/fastq/error_double_qual.fastq            |   22 +
 test/data/fastq/error_double_seq.fastq             |   22 +
 test/data/fastq/error_long_qual.fastq              |   20 +
 test/data/fastq/error_no_qual.fastq                |   20 +
 test/data/fastq/error_qual_del.fastq               |   20 +
 test/data/fastq/error_qual_escape.fastq            |   20 +
 test/data/fastq/error_qual_null.fastq              |  Bin 0 -> 610 bytes
 test/data/fastq/error_qual_space.fastq             |   21 +
 test/data/fastq/error_qual_tab.fastq               |   21 +
 test/data/fastq/error_qual_unit_sep.fastq          |   20 +
 test/data/fastq/error_qual_vtab.fastq              |   20 +
 test/data/fastq/error_short_qual.fastq             |   20 +
 test/data/fastq/error_spaces.fastq                 |   20 +
 test/data/fastq/error_tabs.fastq                   |   21 +
 test/data/fastq/error_trunc_at_plus.fastq          |   19 +
 test/data/fastq/error_trunc_at_qual.fastq          |   19 +
 test/data/fastq/error_trunc_at_seq.fastq           |   18 +
 test/data/fastq/error_trunc_in_plus.fastq          |   19 +
 test/data/fastq/error_trunc_in_qual.fastq          |   20 +
 test/data/fastq/error_trunc_in_seq.fastq           |   18 +
 test/data/fastq/error_trunc_in_title.fastq         |   17 +
 .../fastq/illumina_full_range_as_illumina.fastq    |    8 +
 .../data/fastq/illumina_full_range_as_sanger.fastq |    8 +
 .../data/fastq/illumina_full_range_as_solexa.fastq |    8 +
 .../illumina_full_range_original_illumina.fastq    |    8 +
 test/data/fastq/longreads_as_illumina.fastq        |   40 ++
 test/data/fastq/longreads_as_sanger.fastq          |   40 ++
 test/data/fastq/longreads_as_solexa.fastq          |   40 ++
 test/data/fastq/longreads_original_sanger.fastq    |  120 ++++
 test/data/fastq/misc_dna_as_illumina.fastq         |   16 +
 test/data/fastq/misc_dna_as_sanger.fastq           |   16 +
 test/data/fastq/misc_dna_as_solexa.fastq           |   16 +
 test/data/fastq/misc_dna_original_sanger.fastq     |   16 +
 test/data/fastq/misc_rna_as_illumina.fastq         |   16 +
 test/data/fastq/misc_rna_as_sanger.fastq           |   16 +
 test/data/fastq/misc_rna_as_solexa.fastq           |   16 +
 test/data/fastq/misc_rna_original_sanger.fastq     |   16 +
 .../data/fastq/sanger_full_range_as_illumina.fastq |    8 +
 test/data/fastq/sanger_full_range_as_sanger.fastq  |    8 +
 test/data/fastq/sanger_full_range_as_solexa.fastq  |    8 +
 .../fastq/sanger_full_range_original_sanger.fastq  |    8 +
 .../data/fastq/solexa_full_range_as_illumina.fastq |    8 +
 test/data/fastq/solexa_full_range_as_sanger.fastq  |    8 +
 test/data/fastq/solexa_full_range_as_solexa.fastq  |    8 +
 .../fastq/solexa_full_range_original_solexa.fastq  |    8 +
 test/data/fastq/wrapping_as_illumina.fastq         |   12 +
 test/data/fastq/wrapping_as_sanger.fastq           |   12 +
 test/data/fastq/wrapping_as_solexa.fastq           |   12 +
 test/data/fastq/wrapping_original_sanger.fastq     |   24 +
 test/unit/bio/db/test_fastq.rb                     |  711 ++++++++++++++++++++
 51 files changed, 1652 insertions(+), 0 deletions(-)
 create mode 100644 test/data/fastq/error_diff_ids.fastq
 create mode 100644 test/data/fastq/error_double_qual.fastq
 create mode 100644 test/data/fastq/error_double_seq.fastq
 create mode 100644 test/data/fastq/error_long_qual.fastq
 create mode 100644 test/data/fastq/error_no_qual.fastq
 create mode 100644 test/data/fastq/error_qual_del.fastq
 create mode 100644 test/data/fastq/error_qual_escape.fastq
 create mode 100644 test/data/fastq/error_qual_null.fastq
 create mode 100644 test/data/fastq/error_qual_space.fastq
 create mode 100644 test/data/fastq/error_qual_tab.fastq
 create mode 100644 test/data/fastq/error_qual_unit_sep.fastq
 create mode 100644 test/data/fastq/error_qual_vtab.fastq
 create mode 100644 test/data/fastq/error_short_qual.fastq
 create mode 100644 test/data/fastq/error_spaces.fastq
 create mode 100644 test/data/fastq/error_tabs.fastq
 create mode 100644 test/data/fastq/error_trunc_at_plus.fastq
 create mode 100644 test/data/fastq/error_trunc_at_qual.fastq
 create mode 100644 test/data/fastq/error_trunc_at_seq.fastq
 create mode 100644 test/data/fastq/error_trunc_in_plus.fastq
 create mode 100644 test/data/fastq/error_trunc_in_qual.fastq
 create mode 100644 test/data/fastq/error_trunc_in_seq.fastq
 create mode 100644 test/data/fastq/error_trunc_in_title.fastq
 create mode 100644 test/data/fastq/illumina_full_range_as_illumina.fastq
 create mode 100644 test/data/fastq/illumina_full_range_as_sanger.fastq
 create mode 100644 test/data/fastq/illumina_full_range_as_solexa.fastq
 create mode 100644 test/data/fastq/illumina_full_range_original_illumina.fastq
 create mode 100644 test/data/fastq/longreads_as_illumina.fastq
 create mode 100644 test/data/fastq/longreads_as_sanger.fastq
 create mode 100644 test/data/fastq/longreads_as_solexa.fastq
 create mode 100644 test/data/fastq/longreads_original_sanger.fastq
 create mode 100644 test/data/fastq/misc_dna_as_illumina.fastq
 create mode 100644 test/data/fastq/misc_dna_as_sanger.fastq
 create mode 100644 test/data/fastq/misc_dna_as_solexa.fastq
 create mode 100644 test/data/fastq/misc_dna_original_sanger.fastq
 create mode 100644 test/data/fastq/misc_rna_as_illumina.fastq
 create mode 100644 test/data/fastq/misc_rna_as_sanger.fastq
 create mode 100644 test/data/fastq/misc_rna_as_solexa.fastq
 create mode 100644 test/data/fastq/misc_rna_original_sanger.fastq
 create mode 100644 test/data/fastq/sanger_full_range_as_illumina.fastq
 create mode 100644 test/data/fastq/sanger_full_range_as_sanger.fastq
 create mode 100644 test/data/fastq/sanger_full_range_as_solexa.fastq
 create mode 100644 test/data/fastq/sanger_full_range_original_sanger.fastq
 create mode 100644 test/data/fastq/solexa_full_range_as_illumina.fastq
 create mode 100644 test/data/fastq/solexa_full_range_as_sanger.fastq
 create mode 100644 test/data/fastq/solexa_full_range_as_solexa.fastq
 create mode 100644 test/data/fastq/solexa_full_range_original_solexa.fastq
 create mode 100644 test/data/fastq/wrapping_as_illumina.fastq
 create mode 100644 test/data/fastq/wrapping_as_sanger.fastq
 create mode 100644 test/data/fastq/wrapping_as_solexa.fastq
 create mode 100644 test/data/fastq/wrapping_original_sanger.fastq
 create mode 100644 test/unit/bio/db/test_fastq.rb

commit 951d8f7303a5c28783a2c8b25c9fb347730c1a8f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Oct 11 19:10:15 2009 +0900

    Bio::Fastq API changed.
    
     * Bio::Fastq API changed. Removed methods: phred_quality, solexa_quality.
       New methods: qualities, error_probabilities, format, format=,
       validate_format.
     * New exception classes Bio::Fastq::Error::* for errors.
     * Internal structure is also changed. Internal only classes
       Bio::Fastq::FormatData::* which store parameters for format variants.

 lib/bio/db/fastq.rb |  519 +++++++++++++++++++++++++++++++++++++++++++++++++--
 1 files changed, 501 insertions(+), 18 deletions(-)

commit 9bb7f6ca762c615e50d98c35b60982a4caeea323
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 25 23:36:13 2009 +0900

    Bug fix: infinite loop in Bio::Fastq.new. Thanks to Hiroyuki Mishima for reporting the bug.

 lib/bio/db/fastq.rb |   16 ++++++++++------
 1 files changed, 10 insertions(+), 6 deletions(-)

commit fca6aa5333a95db4dc87e8fc814bd028d5720de4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 20 11:52:33 2009 +0900

    Added file format autodetection for Bio::Fastq

 lib/bio/io/flatfile/autodetection.rb |    6 ++++++
 1 files changed, 6 insertions(+), 0 deletions(-)

commit 1ba21545e7d49ae8b775fbed7a4e92b1daa54ac6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 20 11:48:59 2009 +0900

    Added autoload for Bio::Fastq

 lib/bio.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 380b99106d4c7955b9d07ee8668b53d384c974f4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Mar 19 17:07:25 2009 +0900

    Newly added FASTQ format parser (still a prototype)

 lib/bio/db/fastq.rb |  162 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 162 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/fastq.rb

commit 2c5df2a5f1b5ae1ea9e61c1dccc8bcd2f496f6ce
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Sep 20 19:08:55 2009 +0900

    Removed "require 'rubygems'".

 lib/bio/db/phyloxml/phyloxml_parser.rb |    2 --
 1 files changed, 0 insertions(+), 2 deletions(-)

commit 67818d2550e5d53eeee0f3d710f66f7506fb8127
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Sep 19 17:06:21 2009 +0900

    Use Bio::PubMed.esearch and efetch, etc.
    
     * Changed to use Bio::PubMed.esearch and efetch instead of
       deprecated methods.
     * Regular expression for extracting option is changed.

 sample/pmfetch.rb  |   15 +++++++++++----
 sample/pmsearch.rb |   17 +++++++++++++----
 2 files changed, 24 insertions(+), 8 deletions(-)

commit 0c95889bf69e3140b5f09ade1203d50136aee014
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 18 17:58:17 2009 +0900

    Changed to use temporary directory when writing a file, etc.
    
      * To avoid unexpected file corruption and possibly security risk,
        changed to use temporary directory when writing files. The
        temporary directory is normally removed when all tests end.
        To prevent removing the directory, set environment variable
        BIORUBY_TEST_DEBUG.
      * To avoid test class name conflict, TestPhyloXMLData is renamed
        to TestPhyloXMLWriterData.
      * Added a new test to check existence of libxml-ruby, and removed
        code to raise error when it is not found. The code of the new
        test is completely the same as of in test_phyloxml.rb, but it
        is added for the purpose when test_phyloxml_writer.rb is called
        independently.

 test/unit/bio/db/test_phyloxml_writer.rb |  161 +++++++++++++++++++++---------
 1 files changed, 112 insertions(+), 49 deletions(-)

commit 520d0f5ed535f621aed60b71d8765a99e97306a6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Sep 20 18:34:19 2009 +0900

    Newly added internal-only class Bio::Command::Tmpdir to handle temporary directory
    
     * Newly added internal-only class Bio::Command::Tmpdir to handle
       temporary directory. It is BioRuby library internal use only.
     * Bio::Command.mktmpdir is changed to be completely compatible
       with Ruby 1.9.x's Dir.mktmpdir.

 lib/bio/command.rb                  |  104 +++++++++++++++++++++++++++++++---
 test/functional/bio/test_command.rb |   49 ++++++++++++++++
 2 files changed, 143 insertions(+), 10 deletions(-)

commit c813b60ae62f44d9688b21d47c84e4b7083547e6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 18 17:55:14 2009 +0900

    Added new test to check existence of libxml-ruby, instead of raising error.

 test/unit/bio/db/test_phyloxml.rb |   30 ++++++++++++++++++++----------
 1 files changed, 20 insertions(+), 10 deletions(-)

commit 1b71dd9624640f3f775baab360eef0be92a86677
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Fri Sep 18 21:43:18 2009 -0400

    Renamed output files generated by phyloxml_writer unit tests.

 test/unit/bio/db/test_phyloxml_writer.rb |   13 ++++++++++---
 1 files changed, 10 insertions(+), 3 deletions(-)

commit f8e138cb9e28996f1024fa9cf7c68c8f08603941
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Fri Sep 18 21:33:35 2009 -0400

    Added ncbi_taxonomy_mollusca_short.xml test file

 .../data/phyloxml/ncbi_taxonomy_mollusca_short.xml |   65 ++++++++++++++++++++
 1 files changed, 65 insertions(+), 0 deletions(-)
 create mode 100644 test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml

commit be1be310b7581928581cde24303fe2e16c04e82f
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Fri Sep 18 21:29:20 2009 -0400

    Made the code compactible with libxml-ruby 1.1.3 (previous was 0.9.4) version.

 lib/bio/db/phyloxml/phyloxml_elements.rb |   58 +++++++++++++++---------------
 lib/bio/db/phyloxml/phyloxml_parser.rb   |   10 ++++-
 lib/bio/db/phyloxml/phyloxml_writer.rb   |    8 +++--
 3 files changed, 42 insertions(+), 34 deletions(-)

commit a3441afd5650069a5ada64b202a0714e8723e911
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Tue May 26 00:55:47 2009 -0400

    Newly added PhyloXML support written by Diana Jaunzeikare.
    
     * Newly added PhyloXML support written by Diana Jaunzeikare.
       It have been written during the Google Summer of Code 2009
       "Implementing phyloXML support in BioRuby", mentored by
       Christian Zmasek et al. with NESCent. For details of development,
       see git://github.com/latvianlinuxgirl/bioruby.git and BioRuby
       mailing list archives.
     * This is a combination of 119 commits. The last commit date was
       Mon Aug 17 10:30:10 2009 -0400.

 README.rdoc                              |    3 +
 doc/Tutorial.rd                          |  120 ++-
 lib/bio.rb                               |    6 +
 lib/bio/db/phyloxml/phyloxml.xsd         |  573 ++++++++
 lib/bio/db/phyloxml/phyloxml_elements.rb | 1160 +++++++++++++++++
 lib/bio/db/phyloxml/phyloxml_parser.rb   |  767 +++++++++++
 lib/bio/db/phyloxml/phyloxml_writer.rb   |  223 ++++
 test/data/phyloxml/apaf.xml              |  666 ++++++++++
 test/data/phyloxml/bcl_2.xml             | 2097 ++++++++++++++++++++++++++++++
 test/data/phyloxml/made_up.xml           |  144 ++
 test/data/phyloxml/phyloxml_examples.xml |  415 ++++++
 test/unit/bio/db/test_phyloxml.rb        |  619 +++++++++
 test/unit/bio/db/test_phyloxml_writer.rb |  258 ++++
 13 files changed, 7050 insertions(+), 1 deletions(-)
 create mode 100644 lib/bio/db/phyloxml/phyloxml.xsd
 create mode 100644 lib/bio/db/phyloxml/phyloxml_elements.rb
 create mode 100644 lib/bio/db/phyloxml/phyloxml_parser.rb
 create mode 100644 lib/bio/db/phyloxml/phyloxml_writer.rb
 create mode 100644 test/data/phyloxml/apaf.xml
 create mode 100644 test/data/phyloxml/bcl_2.xml
 create mode 100644 test/data/phyloxml/made_up.xml
 create mode 100644 test/data/phyloxml/phyloxml_examples.xml
 create mode 100644 test/unit/bio/db/test_phyloxml.rb
 create mode 100644 test/unit/bio/db/test_phyloxml_writer.rb

commit fd8281f03423ddf23f7d409863b4df647f1b1564
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 9 21:08:15 2009 +0900

    Newly added Chromatogram classes contributed by Anthony Underwood.
    
     * Newly added Chromatogram classes contributed by Anthony Underwood.
       See git://github.com/aunderwo/bioruby.git for details of development
       before this merge.

 lib/bio.rb                                         |    3 +
 lib/bio/db/chromatogram.rb                         |  133 +++++++++++++
 lib/bio/db/chromatogram/abi.rb                     |  111 +++++++++++
 .../db/chromatogram/chromatogram_to_biosequence.rb |   32 +++
 lib/bio/db/chromatogram/scf.rb                     |  207 ++++++++++++++++++++
 lib/bio/sequence/adapter.rb                        |    1 +
 test/data/chromatogram/test_chromatogram_abi.ab1   |  Bin 0 -> 228656 bytes
 .../data/chromatogram/test_chromatogram_scf_v2.scf |  Bin 0 -> 47503 bytes
 .../data/chromatogram/test_chromatogram_scf_v3.scf |  Bin 0 -> 47503 bytes
 test/unit/bio/db/test_chromatogram.rb              |   99 ++++++++++
 10 files changed, 586 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/chromatogram.rb
 create mode 100644 lib/bio/db/chromatogram/abi.rb
 create mode 100644 lib/bio/db/chromatogram/chromatogram_to_biosequence.rb
 create mode 100644 lib/bio/db/chromatogram/scf.rb
 create mode 100644 test/data/chromatogram/test_chromatogram_abi.ab1
 create mode 100644 test/data/chromatogram/test_chromatogram_scf_v2.scf
 create mode 100644 test/data/chromatogram/test_chromatogram_scf_v3.scf
 create mode 100644 test/unit/bio/db/test_chromatogram.rb

commit 78f9463b764687401ff4a7480c1383c5594e5133
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 10 12:38:25 2009 +0900

    Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".

 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit e731c6e52bc9a672e4546eeca4f2d2d968bdba09
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 2 15:24:00 2009 +0900

    BioRuby 1.3.1 is released.
    
    ChangeLog is modified, and bioruby.gemspec is regenerated.

 ChangeLog       |   11 +++++++++++
 bioruby.gemspec |    2 +-
 2 files changed, 12 insertions(+), 1 deletions(-)
