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Commits on Feb 13, 2008
  1. Tutorial

    Pjotr Prins committed Feb 13, 2008
Commits on Feb 12, 2008
  1. * Bug fixes reported by Shuji Shigenobu.

    ngoto committed Feb 12, 2008
      * Failed to parse query length for long query (>= 10000 letters)
        because comma is inserted for digit separator by blastall.
      * Failed to parse e-value for some BLASTX results
Commits on Feb 11, 2008
  1. Minor adjustments to Tutorial

    Pjotr Prins committed Feb 11, 2008
  2. Expanding on the Tutorial

    Pjotr Prins committed Feb 11, 2008
Commits on Feb 6, 2008
  1. Simple example to translate any NA to AA fasta

    Pjotr Prins committed Feb 6, 2008
Commits on Feb 5, 2008
  1. Fixed broken require in gb2fasta example

    Pjotr Prins committed Feb 5, 2008
  2. Minor tweak to Tutorial.rd

    Pjotr Prins committed Feb 5, 2008
Commits on Feb 3, 2008
  1. More doctests in Tutorial.rd

    Pjotr Prins committed Feb 3, 2008
Commits on Feb 2, 2008
  1. Modified tutorial

    Pjotr Prins committed Feb 2, 2008
  2. Updating tutorial

    Pjotr Prins committed Feb 2, 2008
  3. fix typo

    ktym committed Feb 2, 2008
  4. * lib/bio/shell/rails/vendor/plugins/

    ktym committed Feb 2, 2008
    The 'generators' directory is moved under the 'bioruby' subdirectory
    so that 'bioruby --rails' command can work with Rails 2.x series
    in addition to the Rails 1.2.x series.
Commits on Jan 30, 2008
Commits on Jan 10, 2008
  1. Added a method Bio::EMBOSS.run(program, arguments...)

    ngoto committed Jan 10, 2008
    and Bio::EMBOSS.new is obsoleted.
Commits on Jan 9, 2008
  1. * Bio::Hinv is added

    ktym committed Jan 9, 2008
Commits on Dec 29, 2007
Commits on Dec 28, 2007
  1. Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and

    ngoto committed Dec 28, 2007
    Bio::PDB::Record.create_definition_hash (Note: they should only
    be internally used by PDB parser and users should not call them)
    are changed to follow the change of Module#constants which
    returns an array of Symbol instead of String.
  2. Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit

    ngoto committed Dec 28, 2007
    argument passing of super from method defined by define_method()
    is not supported. Specify all arguments explicitly." error.
Commits on Dec 27, 2007
  1. (ruby 1.9 comliant) in window_search method, changed to avoid shadowing

    ngoto committed Dec 27, 2007
    of local variable by loop local variable.
  2. Fixed parse error for NCBI BLAST 2.2.17.

    ngoto committed Dec 27, 2007
    Added Default::Report#references and Default::Report::HSP#stat_method methods.
Commits on Dec 26, 2007
  1. changelog for changes of lib/bio/alignment.rb and test/unit/bio/test_…

    ngoto committed Dec 26, 2007
    …alignment.rb are added.
  2. * Ruby 1.9 compliant: in EnumerableExtension#each_window and

    ngoto committed Dec 26, 2007
      OriginalAlignment#index methods, local variable names outside the
      iterator loops are changed not to be shadowed by iterator variables.
    * Warning messages for uninitialized instance variables of
      @gap_regexp, @gap_char, @missing_char, and @seqclass are suppressed.
  3. Ruby 1.9 compliant: The last comma in Array.[] is no longer allowed.

    ngoto committed Dec 26, 2007
    (For example, class A < Array; end; A[ 1, 2, 3, ] raises error in Ruby 1.9.)
Commits on Dec 21, 2007
  1. * In Bio::MEDLINE, doi and pii methods are added to extract DOI and P…

    ktym committed Dec 21, 2007
    …II number from AID field
Commits on Dec 18, 2007
  1. * lib/bio/db/pdb/pdb.rb

    ngoto committed Dec 18, 2007
      Bio::PDB#inspect is added to prevent memory exhaust problem.
      ([BioRuby] Parse big PDB use up all memory)
    
    * lib/bio/db/pdb/model.rb
    
      Added Bio::PDB::Model#inspect.
    
    * lib/bio/db/pdb/chain.rb
    
      Added Bio::PDB::Chain#inspect.
    
    * lib/bio/db/pdb/residue.rb
    
      Added Bio::PDB::Residue#inspect.
      This also affects Bio::PDB::Heterogen#inspect.
Commits on Dec 14, 2007
  1. * prepare for BioRuby 1.2 release

    ktym committed Dec 14, 2007