autoload should not be used for libraries outside bio
rdoc documentation for Bio::KEGG::KGML
New class Bio::KEGG::KGML::Graphics with tests for Bio::KEGG::KGML

 * New class Bio::KEGG::KGML::Graphics for storing a graphics element.
   This fixes https://github.com/bioruby/bioruby/issues/51.
 * Unit tests for Bio::KEGG::KGML are added with mock test data.
 * Improve rdoc documentation for Bio::KEGG::KGML.
 * New method Bio::KEGG::KGML::Reaction#id
 * Attribute methods that were different from the KGML attribute
   names are renamed to the names of the KGML attribute names.
   Old method names are deprecated and are changed to aliases
   and will be removed in the future.
    * Bio::KEGG::KGML::Entry#id (old name: entry_id)
    * Bio::KEGG::KGML::Entry#type (old name: category)
    * Bio::KEGG::KGML::Entry#entry1 (old name: node1)
    * Bio::KEGG::KGML::Entry#entry2 (old name: node2)
    * Bio::KEGG::KGML::Entry#type (old name: rel)
    * Bio::KEGG::KGML::Reaction#name (old name: entry_id)
    * Bio::KEGG::KGML::Reaction#type (old name: direction)
 * Following attribute methods are deprecated because two or more
   graphics elements may exist in an entry element. They will be
   removed in the future.
    * Bio::KEGG::KGML::Entry#label
    * Bio::KEGG::KGML::Entry#shape
    * Bio::KEGG::KGML::Entry#x
    * Bio::KEGG::KGML::Entry#y
    * Bio::KEGG::KGML::Entry#width
    * Bio::KEGG::KGML::Entry#height
    * Bio::KEGG::KGML::Entry#fgcolor
    * Bio::KEGG::KGML::Entry#bgcolor
modified documentation for Bio::KEGG::KGML
Bio::KEGG::KGML#parse_* :use new attribute names

 * In Bio::KEGG::KGML#parse_* (private methods) new attribute method
   names should be used instead of deprecated old names.
Incompatible changes: Bio::KEGG::KGML::Reaction#substrates, products

 * Incompatible changes: Bio::KEGG::KGML::Reaction#substrates and
   Bio::KEGG::KGML::Reaction#products are changed to return an array
   containing Bio::KEGG::KGML::Substrate and Bio::KEGG::KGML::Product
   objects, respectively. The aim of these changes are to store ID
   of substrates and products that were thrown away in the previous
   versions.
Incompatible changes in Bio::KEGG::KGML are documented.

 * Incompatible changes in Bio::KEGG::KGML are documented.
 * Next BioRuby release version will be 1.4.3.
regenerate bioruby.gemspec with rake regemspec
Bug fix: Genomenet remote blast: catch up changes of the server
fix typo
Next bioruby release version will be 1.4.3.
Added link to blastall options reference

 * Added link to blastall options reference.
   Thanks to Gareth Rees who sent a pull request.
   (https://github.com/bioruby/bioruby/pull/49)
suppress warnings: URI.escape/URI.unescape is obsolete
suppress warnings: instance variable @comment not initialized
Modified to follow changes of GenomeNet BLAST site
Suppress warnings in lib/bio/alignment.rb:2322

 * A space is inserted to suppress warnings in lib/bio/alignment.rb:2322.
   * warning: :' after local variable is interpreted as binary operator
   * warning: even though it seems like symbol literal
Suppress warnings: shadowing outer local variable

 * Suppress warnings: shadowing outer local variable.
   Thanks to Andrew Grimm: https://github.com/bioruby/bioruby/pull/64
Improve test and suppress warning: assigned but unused variable
Improve test and suppress warning: assigned but unused variable
Improve tests for BLAST "-m 8" tabular format parser