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

 * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
   Fix https://github.com/bioruby/bioruby/issues/89
.travis.yml: Add 2.1.0 and 2.0.0, remove rbx-XXmode

 * 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 https://github.com/bioruby/bioruby/pull/91
.travis.yml: change ruby versions for tar and gem integration tests

 * 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
.travis.yml: rbx version is changed to 2.2.3

 * rbx version is changed to 2.2.3
 * add dependent gems for rbx platforms, described in
   http://docs.travis-ci.com/user/languages/ruby/
.travis.yml: workaround to avoid error in Ruby 1.8.7 and jruby-18mode

 * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
   (reference: https://github.com/rubygems/rubygems/pull/763 )
Ruby 2.1 workaround: Array#uniq does not always choose the first item

 * Ruby 2.1 workaround: Array#uniq does not always choose the first item.
   Thanks to Andrew Grimm who reported the issue.
   (https://github.com/bioruby/bioruby/issues/92 )
   Note that the behavior change is also regarded as a bug in Ruby and
   is fixed. (https://bugs.ruby-lang.org/issues/9340 )
.travis.yml: fix mistakes
gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci

 * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
 * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
suppress "source :rubygems is deprecated" warning
Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008)

* Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
  Thanks to a researcher who reports the patch via email.
Refactored to shorten, remove rescues, and clarify.
Fixed the stack level too deep errors by using Hash#invert.
Refactor Bio::AminoAcid#weight: Early return clearer and idiomatic.