Added acknowledgement to Kozo Nishida for KEGG parsers.
Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.0.rdoc.
Release notes for the upcoming release version.
New methods Bio::KEGG::GENES#keggclass etc.

 * New methods and aliases are added: Bio::KEGG::GENES#keggclass,
   keggclasses, names_as_array, names, motifs_as_strings,
   motifs_as_hash, motifs.
 * Removed Bio::KEGG::GENES#genes, gene and motif methods.
 * Added a comment about deprecation of CODON_USAGE lines.
 * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb
   (original commit message: Changes for TogoWS).
Reverted Bio::KEGG::GENES#genes, gene and motif methods and modified.

 * Reverted Bio::KEGG::GENES#genes, gene and motif methods which are
   removed in the last commit. To avoid code duplication, they are
   also modified to use other methods, and RDoc is added about the
   deprecation or change of the methods.
 * Modified RDoc.
Modified tests for Bio::KEGG::GENES following the changes of the class.
Renamed Bio::KEGG::*#pathway_modules to modules, etc.

 * Renamed following methods in Bio::KEGG::ORTHOLOGY and
   Bio::KEGG:PATHWAY classes: pathway_modules to modules,
   pathway_modules_as_strings to modules_as_strings, and
   pathway_modules_as_hash to modules_as_hash.
 * Unit tests are also modified.
Private method strings_as_hash is moved to Bio::KEGG::Common::StringsAsHash.
Added methods for parsing KEGG PATHWAY fields.

 * Added methods for parsing KEGG PATHWAY fields.
 * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb
   and modified to merge with the current HEAD (original commit
   message: Changes for TogoWS).
Tests for Bio::KEGG::PATHWAY are improved with new test data.
Test bug fix: confusion between assert and assert_equal, and apparently wrong expected values.

 * Test bug fix: the assert should be assert_equal. The bug was found
   with Ruby 1.9.2-p0.
 * In the test_rates_hundred_and_fiftieth_position method, the index
   for @example_rates and the expected value of the third assertion
   were apparently wrong.
 * Reported by Tomoaki NISHIYAMA during BH2010.10.
Test bug fix: confusion between assert and assert_equal

 * Test bug fix: the assert should be assert_equal. The bug was
   found with Ruby 1.9.2-p0.
Ruby 1.9.2 support: Incompatible change: the symmetric elements for triangular matrix should be copied

 * Ruby 1.9.2 support: Incompatible change: the symmetric elements
   for triangular matrix should be copied. The patch is written by
   Tomoaki NISHIYAMA during BH2010.10.
Changed the expected return values in the unit tests, following the last change to Bio::AAindex2.

 * Changed the expected return values in the unit tests,
 following the last change to Bio::AAindex2.
 * The patch is written by Tomoaki NISHIYAMA during BH2010.10.
Added description about incompatible the change in Bio::AAindex2.
Shows message when running "ruby setup.rb test" with Ruby1.9.
Small changes for README.rdoc.
Ruby 1.9.2 support: using assert_in_delta for float values.

 * Ruby 1.9.2 support: using assert_in_delta for float values.
   The patch is written by Tomoaki NISHIYAMA during BH2010.10.
Ruby 1.9.2 support: assert_in_delta for a float value.
Ruby 1.9.2 support: defined Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands#initialize

 * Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands#initialize
   is explicitly defined, due to the behavior change of argument number
   check in the default initialize method in Ruby 1.9.2.