* 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 ).
* Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008). Thanks to a researcher who reports the patch via email.
* gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
* workaround to avoid error in Ruby 1.8.7 and jruby-18mode (reference: rubygems/rubygems#763 )
* 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
* 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
* Bug fix: Only do gsub on bio_ref.reference.authors if it exists. Fix bioruby#89
…quence * Bug fix: Missing require when generating genbank output for BioSQL sequence. Partly fix bioruby#89
* sample/benchmark_clustalw_report.rb: Benchmark parsing speed of example1-seqnos.aln in addition to example1.aln.
* 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.
* 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.
* 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)
* 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.
* Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB. * Test class names are also changed.