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Commits on Aug 2, 2012
Commits on Jul 27, 2012
  1. @ngoto

    Suppress warnings: shadowing outer local variable

    ngoto authored
     * Suppress warnings: shadowing outer local variable.
       Thanks to Andrew Grimm: bioruby#64
Commits on Jul 25, 2012
  1. @ngoto

    Suppress warnings in lib/bio/alignment.rb:2322

    ngoto authored
     * 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
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Commits on Jul 23, 2012
  1. @ngoto

    Added link to blastall options reference

    ngoto authored
     * Added link to blastall options reference.
       Thanks to Gareth Rees who sent a pull request.
       (bioruby#49)
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    fix typo

    ngoto authored
  4. @ngoto
Commits on Jul 20, 2012
  1. @ngoto
Commits on Jul 18, 2012
  1. @ngoto

    Incompatible changes in Bio::KEGG::KGML are documented.

    ngoto authored
     * Incompatible changes in Bio::KEGG::KGML are documented.
     * Next BioRuby release version will be 1.4.3.
  2. @ngoto

    Incompatible changes: Bio::KEGG::KGML::Reaction#substrates, products

    ngoto authored
     * 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.
  3. @ngoto

    Bio::KEGG::KGML#parse_* :use new attribute names

    ngoto authored
     * In Bio::KEGG::KGML#parse_* (private methods) new attribute method
       names should be used instead of deprecated old names.
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    New class Bio::KEGG::KGML::Graphics with tests for Bio::KEGG::KGML

    ngoto authored
     * New class Bio::KEGG::KGML::Graphics for storing a graphics element.
       This fixes bioruby#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
Commits on Jul 17, 2012
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Commits on Jul 11, 2012
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Commits on Jul 5, 2012
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    Tree output (formatter) methods moved to lib/bio/tree/output.rb

    ngoto authored
     * To avoid circular require about bio/tree, phylogenetic tree output
      (formatter) methods are moved to lib/bio/tree/output.rb.
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  9. @ngoto

    Remove old comment lines

    ngoto authored
  10. @ngoto

    Finalizer for Bio::Command::Tmpdir is changed to suppress test failure

    ngoto authored
     * New class Bio::Command::Tmpdir::Remover for removing temporary
       directory in finilizer. This class is BioRuby internal use only.
       Users should not use this class.
     * Finalizer for Bio::Command::Tmpdir is changed from a Proc object
       to an instance of the Remover class.
     * Test failure fix: In some environment, with Ruby 1.9.2,
       test_output_embl(Bio::FuncTestSequenceOutputEMBL) was failed with
       "<#<ArgumentError: wrong number of arguments (1 for 0)>" that was
       raised in the finalizer callback of Bio::Command::Tmpdir. This
       commit fixes the problem.
  11. @ngoto

    Workaround to avoid circular require and JRuby autoload bug

    ngoto authored
     * "require" lines are modified to avoid circular require.
     * In files that would be required directly from outside bio/sequence
       (aa.rb, adapter.rb, common.rb, compat.rb, dblink.rb, generic.rb,
       na.rb, quality_score.rb, sequence_masker.rb), because of avoiding
       potential mismatch of superclass and/or lack of some methods,
       bio/sequence.rb is required when Bio::Sequence is not defined.
     * workaround to avoid JRuby autoload bug
  12. @ngoto

    workaround to avoid circular require in Bio::RestrictionEnzyme

    ngoto authored
     * Workaround to avoid circular require in Bio::RestrictionEnzyme
     * Special care was needed for Bio::RestrictionEnzyme::Analysis
       because its method definitions are divided into two files:
       analysis.rb, analysis_basic.rb.
  13. @ngoto
Commits on Jul 4, 2012
  1. @ngoto
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  3. @ngoto

    workaround to avoid JRuby autoload bug

    ngoto authored
     * Workaround to avoid JRuby autoload bug.
     * Changed to require bio/db.rb because it is always loaded.
Commits on Jun 28, 2012
  1. @ngoto

    Rakefile: use own mktmpdir

    ngoto authored
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