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Commits on Oct 25, 2014
Commits on Oct 21, 2014
  1. Doc bug fix: wrong sample code

    ngoto committed Oct 21, 2014
  2. Prevent to repeat calculations of total bases

     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
       repeat calculations of total bases.
    ngoto committed Oct 21, 2014
  3. Documentation bug fix: Return value is Rational or Float.

     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Return value
       is Rational or Float in recent versions of Ruby. Documentation added for
       the treatment of "u" and to return 0.0 if there are no bases.
       Reported by ctSkennerton (bioruby#73 ).
    ngoto committed Oct 21, 2014
Commits on Aug 11, 2014
Commits on Aug 5, 2014
  1. Update URIs

     * Update URIs.
     * Remove links to RubyForge and RAA which have already been closed.
     * Add some words for Ruby 1.9 or later.
    ngoto committed Aug 5, 2014
Commits on May 16, 2014
Commits on Mar 19, 2014
  1. Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)

    * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
      Thanks to a researcher who reports the patch via email.
    ngoto committed Mar 19, 2014
Commits on Jan 17, 2014
  1. gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci

     * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
     * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
    ngoto committed Jan 17, 2014
  2. .travis.yml: fix mistakes

    ngoto committed Jan 17, 2014
  3. Ruby 2.1 workaround: Array#uniq does not always choose the first item

     * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
       Thanks to Andrew Grimm who reported the issue.
       (bioruby#92 )
       Note that the behavior change is also regarded as a bug in Ruby and
       is fixed. (https://bugs.ruby-lang.org/issues/9340 )
    ngoto committed Jan 17, 2014
  4. .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode

     * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
       (reference: rubygems/rubygems#763 )
    ngoto committed Jan 17, 2014
  5. .travis.yml: rbx version is changed to 2.2.3

     * rbx version is changed to 2.2.3
     * add dependent gems for rbx platforms, described in
       http://docs.travis-ci.com/user/languages/ruby/
    ngoto committed Jan 17, 2014
Commits on Jan 10, 2014
  1. .travis.yml: change ruby versions for tar and gem integration tests

     * In tar and gem integration tests, Ruby versions are changed to
       MRI 2.0.0 and jruby-19mode.
     * Add jruby-18mode
     * Add rbx-2.1.1
    ngoto committed Jan 10, 2014
Commits on Jan 8, 2014
  1. .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode

     * Add 2.1.0 and 2.0.0
     * Remove rbx-18mode and rbx-19mode
     * 1.9.2 is moved from "include" to "rvm".
     * 1.8.7 is moved from "rvm" to "include", and remove
       "gemfiles/Gemfile.travis-ruby1.8" line from "gemfile".
     * Remove "exclude" and simplify build matrix.
     * Suggested by agrimm in bioruby#91
    ngoto committed Jan 8, 2014
Commits on Dec 10, 2013
  1. Bug fix: Only do gsub on bio_ref.reference.authors if it exists.

     * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
       Fix bioruby#89
    binnisb committed with ngoto Dec 9, 2013
  2. Bug fix: Missing require when generating genbank output for BioSQL se…

    …quence
    
     * Bug fix: Missing require when generating genbank output for BioSQL
       sequence. Partly fix bioruby#89
    binnisb committed with ngoto Dec 9, 2013
Commits on Nov 23, 2013
  1. Benchmark example1-seqnos.aln in addition to example1.aln

     * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
       example1-seqnos.aln in addition to example1.aln.
    ngoto committed Nov 23, 2013
  2. Bio::ClustalW::Report#do_parse speed optimization

     * Bio::ClustalW::Report#do_parse speed optimization. Thanks to
       Andrew Grimm who indicates the optimization point.
       (bioruby#86 )
     * "$" in the regular expression is changed to "\z". In this context,
       the "$" was intended to be matched with only the end of the string.
    ngoto committed Nov 23, 2013
  3. New test data: ClustalW with -SEQNOS=ON option

     * test/data/clustalw/example1-seqnos.aln: New test data: ClustalW
       running with -SEQNOS=ON option.
     * Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
       that parses the above data.
    ngoto committed Nov 23, 2013
  4. Simplify test data path in setup

     * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
       filename path.
     * Modify indentes and void lines.
    ngoto committed Nov 23, 2013
  5. Common test methods are moved to a module

     * New namespace module Bio::TestClustalWReport.
     * Common test methods are moved to CommonTestMethods,
       and test classes using the methods include it.
     * The test_sequences method is split into two methods
       CommonTestMethods#test_sequence0 and test_sequence1.
    ngoto committed Nov 23, 2013
Commits on Aug 23, 2013
  1. Test bug fix: Read test file with binary mode to avoid encoding error

     * Test bug fix: Read test file with binary mode to avoid string encoding
       error. Thanks to nieder (github.com/nieder) who reports the bug.
       (bioruby#84)
    ngoto committed Aug 23, 2013
  2. Modified siRNA design rules by Ui-Tei and Reynolds

     * Ui-Tei rule: Avoided contiguous GCs 10 nt or more.
     * Reynolds rule: Total score of eight criteria is calculated.
       * Returns numerical score for functional siRNA instead of returning 'true'.
       * Returns 'false' for non-functional siRNA, as usual.
     * Unit tests are modified to reflect these changes.
    meso-cacase committed with ngoto Apr 4, 2013
Commits on Jun 28, 2013
  1. Use Bio::UniProtKB instead of Bio::UniProt

     * Use Bio::UniProtKB instead of Bio::UniProt.
     * Test class names are also changed from UniProt to UniProtKB.
    ngoto committed Jun 28, 2013
  2. Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.

     * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
     * Test class names are also changed.
    ngoto committed Jun 28, 2013
  3. Bio::SwissProt and Bio::TrEMBL are deprecated

     * Bio::SwissProt and Bio::TrEMBL are deprecated.
     * Show warning messages when using these classes.
    ngoto committed Jun 28, 2013