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Commits on Dec 28, 2009
  1. BioRuby 1.4.0 is released.

    ngoto committed Dec 28, 2009
  2. ChangeLog is autogenerated from git log.

     * ChangeLog is autogenerated from git log with the following command:
        % git log --stat --summary \
              3d1dfcc..HEAD > ChangeLog
    ngoto committed Dec 28, 2009
  3. The PTS1 Predictor's URL had been changed.

     * The PTS1 Predictor's URL had been changed.
     * Changed to use @uri instead of @host and @cgi_path.
    ngoto committed Dec 28, 2009
  4. Preparation of ChangeLog autogeneration: old ChangeLog is moved to do…

    …c/ChangeLog-before-1.3.1.
    ngoto committed Dec 28, 2009
  5. Tutorial.rd.html is regenerated.

    ngoto committed Dec 28, 2009
  6. Added Bio::NCBI.default_email= in the example, and examples using dep…

    …recated Bio::PubMed methods are temporarily commented out.
    ngoto committed Dec 28, 2009
  7. Tutorial: Added info on how to run rubydoctest

              Removed bioruby> prefix for one failing BLAST test
    pjotrp committed with ngoto Dec 27, 2009
Commits on Dec 25, 2009
Commits on Dec 24, 2009
  1. bioruby.gemspec is regenerated

    ngoto committed Dec 24, 2009
  2. Issues added and modified.

    ngoto committed Dec 24, 2009
  3. New singleton methods Bio::NCBI.default_email=, default_tool=, etc.

     * New singleton methods Bio::NCBI.default_email=, default_email,
       default_tools=, default_tools, etc., because email and tool
       parameters will be mandatory in Entrez eUtils.
     * Changed to raise error when email or tool is empty. Note that
       default email is nil and library users should always set their
       email address.
     * Default tool name is changed to include $0 and bioruby version ID.
     * Added multi-thread support for Bio::NCBI::REST#ncbi_access_wait.
    ngoto committed Dec 24, 2009
Commits on Dec 21, 2009
Commits on Dec 20, 2009
Commits on Dec 15, 2009
  1. New method Bio::KEGG::DRUG#products

     * New method Bio::KEGG::DRUG#products.
     * Improved RDoc.
    ngoto committed Dec 15, 2009
Commits on Dec 10, 2009
  1. Methods in Bio::KEGG::Common::* are changed to cache return values in…

    … instance variables.
    ngoto committed Dec 10, 2009
  2. Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.

     * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the
       method dblinks is changed to return a Hash. The old methods  are
       renamed to dblinks_as_strings.
     * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION,
       the method  pathways is changed to return a Hash. The old methods
       are renamed to pathways_as_strings except for GENES.
     * In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method
       orthologs is changed to return a Hash. The old methods are renamed
       to orthologs_as_strings.
     * Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed
       to return a Hash. The old methods are renamed to genes_as_strings.
     * Added Bio::KEGG::REACTION#rpairs_as_tokens, older behavior of rpairs.
     * Modules in lib/bio/db/kegg/common.rb are moved uner Bio::KEGG::Common
       namespace.
     * Refactoring.
     * Added documents.
     * Tests modified.
    ngoto committed Dec 10, 2009
  3. Bio::KEGG::GENES#structure no more adds PDB: prefix.

     * Bio::KEGG::GENES#structure no more adds PDB: prefix.
     * Added Bio::KEGG::GENES#structures as an alias of structure.
    ngoto committed Dec 10, 2009