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Commits on Oct 25, 2014
Commits on Oct 21, 2014
  1. @ngoto

    Doc bug fix: wrong sample code

    ngoto authored
  2. @ngoto

    Prevent to repeat calculations of total bases

    ngoto authored
     * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
       repeat calculations of total bases.
  3. @ngoto

    Documentation bug fix: Return value is Rational or Float.

    ngoto authored
     * 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 ).
Commits on Aug 11, 2014
  1. @ngoto
Commits on Aug 5, 2014
  1. @ngoto

    Update URIs

    ngoto authored
     * Update URIs.
     * Remove links to RubyForge and RAA which have already been closed.
     * Add some words for Ruby 1.9 or later.
Commits on May 16, 2014
  1. @yb66 @ngoto
  2. @yb66 @ngoto

    Fixed the stack level too deep errors by using Hash#invert.

    yb66 authored ngoto committed
  3. @yb66 @ngoto

    Refactored to shorten, remove rescues, and clarify.

    yb66 authored ngoto committed
Commits on Mar 19, 2014
  1. @ngoto

    Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)

    ngoto authored
    * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
      Thanks to a researcher who reports the patch via email.
Commits on Jan 17, 2014
  1. @ngoto
  2. @ngoto

    gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci

    ngoto authored
     * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
     * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
  3. @ngoto

    .travis.yml: fix mistakes

    ngoto authored
  4. @ngoto

    Ruby 2.1 workaround: Array#uniq does not always choose the first item

    ngoto authored
     * 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 )
  5. @ngoto

    .travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode

    ngoto authored
     * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
       (reference: rubygems/rubygems#763 )
  6. @ngoto

    .travis.yml: rbx version is changed to 2.2.3

    ngoto authored
     * rbx version is changed to 2.2.3
     * add dependent gems for rbx platforms, described in
       http://docs.travis-ci.com/user/languages/ruby/
Commits on Jan 10, 2014
  1. @ngoto

    .travis.yml: change ruby versions for tar and gem integration tests

    ngoto authored
     * 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
Commits on Jan 8, 2014
  1. @ngoto

    .travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode

    ngoto authored
     * 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
Commits on Dec 10, 2013
  1. @binnisb @ngoto

    Bug fix: Only do gsub on bio_ref.reference.authors if it exists.

    binnisb authored ngoto committed
     * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
       Fix bioruby#89
  2. @binnisb @ngoto

    Bug fix: Missing require when generating genbank output for BioSQL se…

    binnisb authored ngoto committed
    …quence
    
     * Bug fix: Missing require when generating genbank output for BioSQL
       sequence. Partly fix bioruby#89
Commits on Nov 23, 2013
  1. @ngoto

    Benchmark example1-seqnos.aln in addition to example1.aln

    ngoto authored
     * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
       example1-seqnos.aln in addition to example1.aln.
  2. @agrimm @ngoto

    Add benchmark script for Bio::ClustalW::Report.

    agrimm authored ngoto committed
  3. @ngoto

    Bio::ClustalW::Report#do_parse speed optimization

    ngoto authored
     * 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.
  4. @ngoto

    New test data: ClustalW with -SEQNOS=ON option

    ngoto authored
     * 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.
  5. @ngoto

    Simplify test data path in setup

    ngoto authored
     * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
       filename path.
     * Modify indentes and void lines.
  6. @ngoto

    Common test methods are moved to a module

    ngoto authored
     * 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.
Commits on Aug 23, 2013
  1. @ngoto

    Test bug fix: Read test file with binary mode to avoid encoding error

    ngoto authored
     * 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)
  2. @meso-cacase @ngoto

    Modified siRNA design rules by Ui-Tei and Reynolds

    meso-cacase authored ngoto committed
     * 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.
Commits on Jun 28, 2013
  1. @ngoto

    Use Bio::UniProtKB instead of Bio::UniProt

    ngoto authored
     * Use Bio::UniProtKB instead of Bio::UniProt.
     * Test class names are also changed from UniProt to UniProtKB.
  2. @ngoto
  3. @ngoto

    Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.

    ngoto authored
     * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
     * Test class names are also changed.
  4. @ngoto
  5. @ngoto
  6. @ngoto

    Bio::SwissProt and Bio::TrEMBL are deprecated

    ngoto authored
     * Bio::SwissProt and Bio::TrEMBL are deprecated.
     * Show warning messages when using these classes.
  7. @ngoto
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