Remove descriptions about DDBJ Web API (WABI)
Bio::RefSeq and Bio::DDBJ are deprecated. Show warnings.

 * 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.
Rename lib/bio/db/embl/sptr.rb to uniprotkb.rb
Bio::SPTR is renamed as Bio::UniProtKB and changed to an alias

 * Bio::SPTR is renamed to Bio::UniProtKB.
 * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
   Bio::UniProtKB.
Bio::UniProt is changed to be an alias of Bio::UniProtKB.
Bio::SwissProt and Bio::TrEMBL are deprecated

 * Bio::SwissProt and Bio::TrEMBL are deprecated.
 * Show warning messages when using these classes.
Add autoload of Bio::UniProtKB, and modify comments of deprecated classes.
test_sptr.rb is renamed to test_uniprotkb.rb
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.
rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
Use Bio::UniProtKB instead of Bio::UniProt

 * Use Bio::UniProtKB instead of Bio::UniProt.
 * Test class names are also changed from UniProt to UniProtKB.
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.
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.
   (https://github.com/bioruby/bioruby/issues/84)
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.
Simplify test data path in setup

 * Bio::TestClustalWReport::TestClustalWReport#setup: simplify test data
   filename path.
 * Modify indentes and void lines.
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.
Bio::ClustalW::Report#do_parse speed optimization

 * Bio::ClustalW::Report#do_parse speed optimization. Thanks to
   Andrew Grimm who indicates the optimization point.
   (https://github.com/bioruby/bioruby/pull/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.
Add benchmark script for Bio::ClustalW::Report.
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.
Bug fix: Missing require when generating genbank output for BioSQL sequence

 * Bug fix: Missing require when generating genbank output for BioSQL
   sequence. Partly fix https://github.com/bioruby/bioruby/issues/89