* 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.
* Ruby 2.1 workaround: Array#uniq does not always choose the first item. Thanks to Andrew Grimm who reported the issue. (#92 ) Note that the behavior change is also regarded as a bug in Ruby and is fixed. (https://bugs.ruby-lang.org/issues/9340 )
* workaround to avoid error in Ruby 1.8.7 and jruby-18mode (reference: rubygems/rubygems#763 )
* rbx version is changed to 2.2.3 * add dependent gems for rbx platforms, described in http://docs.travis-ci.com/user/languages/ruby/
* 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 #91
* Bug fix: Only do gsub on bio_ref.reference.authors if it exists. Fix #89
…quence * Bug fix: Missing require when generating genbank output for BioSQL sequence. Partly fix #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. (#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.
* 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.
* Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data filename path. * Modify indentes and void lines.
* 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. (#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.
* Use Bio::UniProtKB instead of Bio::UniProt. * Test class names are also changed from UniProt to UniProtKB.
* Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB. * Test class names are also changed.
* Bio::SwissProt and Bio::TrEMBL are deprecated. * Show warning messages when using these classes.
* Bio::SPTR is renamed to Bio::UniProtKB. * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of Bio::UniProtKB.
* Bio::RefSeq and Bio::DDBJ are deprecated because they were only an alias of Bio::GenBank. Please use Bio::GenBank instead. * Show warning message when loading the classes and initializing a new instance. * Changed to require genbank.rb only when GenBank is not defined. This might reduce the possibility of circular require.
* Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components which use Bio::DDBJ::XML or Bio::DDBJ::REST.
* Remove Bio::DDBJ::XML and Bio::DDBJ::REST due to suspension of DDBJ Web API (WABI). DDBJ says that it is now under reconstruction and the API will be completely changed. Thus, I've decided to throw away current API client in Ruby and to implement new one with the new API. * Autoload lines in lib/bio/db/genbank/ddbj.rb are removed. * Tests are also removed.