Bug fix: Bio::FastaFormat#query passes nil to the given factory

 * Bug fix: Bio::FastaFormat#query passes nil to the given factory
   object. Thanks to Philipp Comans who reports the bug.
   (https://github.com/bioruby/bioruby/issues/35)
 * Test method for Bio::FastaFormat#query is added.
Added a test for Bio::FastaFormat#entry_overrun etc.

 * Added a test for Bio::FastaFormat#entry_overrun.
 * Removed a void test class.
A sample benchmark script for Bio::RestrictionEnzyme::Analysis.cut
New classes (for internal use only) for restriction enzyme classes

 * New classes Bio::RestrictionEnzyme::SortedNumArray and
   Bio::RestrictionEnzyme::DenseIntArray. Both of them are for
   Bio::RestrictionEnzyme internal use only. They will be used
   for the speedup of restriction enzyme analysis.
Speedup of Bio::RestrictionEnzyme::Analysis.cut.

 * Speedup of Bio::RestrictionEnzyme::Analysis.cut. The new code
   is 50 to 80 fold faster than the previous code when cutting
   1Mbp sequence running on Ruby 1.9.2p180.
 * Thanks to Tomoaki NISHIYAMA who wrote the first version of the
   patch. Thanks to ray1729 (on GitHub) who reports the issue.
   (https://github.com/bioruby/bioruby/issues/10)
Added topics for the release notes
README.rdoc: changed required Ruby version etc.

 * README.rdoc: now Ruby 1.8.6 or later is required.
 * README.rdoc: removed old obsolete descriptions.
 * README.rdoc: modified about RubyGems.
 * KNOWN_ISSUES.rdoc: moved descriptions about older RubyGems and CVS
   from README.rdoc.
 * KNOWN_ISSUES.rdoc: modified about end-of-life Ruby versions.
RELEASE_NOTES.rdoc is updated following recent changes.
Test bug fix: use sort command in PATH

 * Test bug fix: FuncTestCommandQuery: use sort command in PATH.
   Thanks to Tomoaki Nishiyama who reports the issue.
   (https://github.com/bioruby/bioruby/pull/13)
preparation for release: alpha test version 1.4.2-alpha1
Bug fix: Bio::SPTR follow-up of UniProtKB format changes

 * Bug fix: Bio::SPTR follow-up of UniProtKB format changes.
 * Tests are added about the fix.
 * Bug fix: Bio::SPTR#cc_web_resource should be private.
 * Incompatible changes in Bio::SPTR#cc("WEB RESOURCE") is
   documented in RELEASE_NOTES.rdoc.
 * KNOWN_ISSUES.rdoc: description about incompleteness of the fix.
 * Thanks to Nicholas Letourneau who reports the issue.
   (https://github.com/bioruby/bioruby/pull/36)
In Fastq formatter, default width value changed to nil

 * In Bio::Sequence#output(:fastq) (Fastq output formatter),
   default width value is changed from 70 to nil, which means
   "without wrapping".  close [Feature #3191]
   (https://redmine.open-bio.org/issues/3191)
Bio::DDBJ::REST::*. new classes for DDBJ REST web services.

 * Bio::DDBJ::REST::*: new classes for DDBJ REST web services (WABI).
   Currently not all services are covered. (lib/bio/io/ddbjrest.rb)
 * autoload of the above (lib/bio/db/genbank/ddbj.rb, lib/bio.rb)
 * Tests for the above (but still incomplete)
   (test/functional/bio/io/test_ddbjrest.rb)
 * Remote BLAST using DDBJ server now uses REST interface instead
   of SOAP, for Ruby 1.9.x support.
   (lib/bio/appl/blast/ddbj.rb)
A test connecting to DDBJ BLAST web service is enabled.
RELEASE_NOTES.rdoc changed to reflect recent changes.
New method Bio::Fastq#to_s

 * New method Bio::Fastq#to_s.
   Thanks to Tomoaki NISHIYAMA who wrote a patch.
   (https://github.com/bioruby/bioruby/pull/37)
New methods Bio::NCBI::REST::EFetch.nucleotide and protein

 * New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
   to get data from "nucleotide" and "protein" database respectively.
   Because NCBI changed not to accept "gb" format for the database
   "sequence", the two new methods are added for convenience.
 * In BioRuby Shell, efetch method uses the above new methods.
In BioRuby Shell, getent() fails when EMBOSS seqret does not found.
RELEASE_NOTE.rdoc modified to reflect recent changes
fix typo and change order of lines