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Commits on Jul 18, 2007
  1. * Changed method names:

      1. reports_in_* -> parse_*
      2. parse_in_* -> parse_*_entry
      3. to_* -> format_*
    * Added Report#output(:format_type) method to be the facade pattern of
      format_* methods.
    nakao committed Jul 18, 2007
  2. changed messages and documents

    ngoto committed Jul 18, 2007
Commits on Jul 17, 2007
Commits on Jul 16, 2007
  1. * autoloadified

    ktym committed Jul 16, 2007
  2. * fixed that get_dsn.each {|dsn| dsn.mapmaster} to return correct

      value (mapmaster URL). This bug is fixed and reported by Dave Thorne
      on bioruby list on June 7, 2007.
    ktym committed Jul 16, 2007
  3. documents are added

    ngoto committed Jul 16, 2007
  4. Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified

    to follow Bio::Alignment::FactoryTemplate (but not yet changed to use it).
    ngoto committed Jul 16, 2007
  5. New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added

    for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
    Contributed by Jeffrey Blakeslee and colleagues.
    ngoto committed Jul 16, 2007
  6. * lib/bio/mafft/report.rb

      For generic multi-fasta formatted sequence alignment,
      Bio::Alignment::MultiFastaFormat is newly added based on
      Bio::MAFFT::Report class, and Bio::MAFFT::Report is
      changed to inherit the new class.
      Tests are added in test/unit/bio/appl/mafft/test_report.rb.
    * lib/bio/alignment.rb
      added autoload of Bio::Alignment::MultiFastaFormat.
      New modules and classes Bio::Alignment::FactoryTemplate::* are added.
    ngoto committed Jul 16, 2007
Commits on Jul 10, 2007
  1. Pdb_LString.new is changed not to raise error for nil.

    Fixed a bug when below records does not exist in a PDB entry:
    REMARK (remark), JRNL (jrnl), HELIX (helix),
    TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
    DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
    HEADER (entry_id, accession, classification),
    TITLE (definition), and REVDAT (version) records (methods).
    
    Incompatible change: Bio::PDB#record is changed to return
    an empty array for nonexistent record.
    
    Thanks to Dr. Mikael Borg. (Re: [BioRuby] Preparing for 1.1 release)
    ngoto committed Jul 10, 2007
Commits on Jul 9, 2007
  1. Updated tutorial to include generating a random sequence and an example

    of using the rebase library.
    Pjotr Prins committed Jul 9, 2007
  2. * images are renamed to be prefixed by 'bioruby-' to avoid confliction

      with already existing files in /public/images
    ktym committed Jul 9, 2007
  3. * Completely new design for BioRuby shell on Rails translated from

      the 'DibdoltRed' theme on www.openwebdesign.org which is created by
      Darjan Panic and Brian Green as a public domain work.
    ktym committed Jul 9, 2007
  4. * Bio::KEGG::Taxonomy class which treats taxonomyc tree structure of the

      KEGG taxonomy file available at ftp.genome.jp/pub/kegg/genes/taxonomy
      which is a replacement of the previously keggtab file (Bio::KEGG::Keggtab).
    ktym committed Jul 9, 2007
Commits on Jun 28, 2007
  1. * utilize field_fetch

    ktym committed Jun 28, 2007
  2. * fixed to accept absolute path in the command line option of the ses…

    …sion
    
      storing directory. e.g. following 2 examples run as expected.
    
        $ bioruby foo/bar
        $ bioruby /tmp/foo/bar
    
    * Bio::Shell.cache[:savedir] always stores the bioruby shell storing directory,
      Bio::Shell.cache[:workdir] always stores the working directory at start up
      (both are converted to full path allowing user to use Dir.chdir in the
      shell session).
    
    * if --rails (-r) option is applied, bioruby command will run in the rails mode,
      and rails server will start in the :savedir, otherwise run in the current
      directory in the irb mode.
    
    Note: "session" means shell/session/{config,history,object} files
    in the following explanations.
    
    === IRB mode ===
    
    1. run in the current directory and the session will be saved
       in the ~/.bioruby directory
    
         $ bioruby
    
    2. run in the current directory and the session will be saved
       in the foo/bar directory
    
         $ bioruby foo/bar
    
    3. run in the current directory and the session will be saved
       in the /tmp/foo/bar directory
    
         $ bioruby /tmp/foo/bar
    
    === Rails mode ===
    
    4. run in the ~/.bioruby directory and the session will be also saved
       in the ~/.bioruby directory
    
        $ bioruby -r
    
    5. run in the foo/bar directory and the session will be also saved
       in the foo/bar directory
    
        $ bioruby -r foo/bar
    
    6. run in the /tmp/foo/bar directory and the session will be also saved
       in the /tmp/foo/bar directory
    
        $ bioruby -r /tmp/foo/bar
    
    === Script mode ===
    
    7. run in the current directory using the session saved
       in the ~/.bioruby directory.
    
        $ bioruby ~/.bioruby/shell/script.rb
    
    7'. run in the current directory using the session saved
       in the foo/bar directory.
    
        $ bioruby foo/bar/shell/script.rb
    
    7''. run in the current directory using the session saved
       in the /tmp/foo/bar directory.
    
        $ bioruby /tmp/foo/bar/shell/script.rb
    
    Essentially, no difference among these three (7, 7', and 7'') examples.
    ktym committed Jun 28, 2007
  3. * added bioruby logo

    * if rails is started with ~/.bioruby, show Dir.pwd as a project dir
      instead of ".bioruby" (meaningless, although), otherwise show
      savedir as a "Project" directory in the left pane.
    ktym committed Jun 28, 2007
  4. * bioruby logo

    ktym committed Jun 28, 2007
Commits on Jun 26, 2007
  1. * changed to show leaf directory name of the session at Project section

      and linked to the real directory with file:// protocol
    ktym committed Jun 26, 2007
  2. * changed to cache full path of the save directory and avoid to use

      Dir.chdir, so that user can freely use Dir.chdir in the shell
      environment without affecting saving session functionality
    ktym committed Jun 26, 2007
Commits on Jun 20, 2007
  1. * user interface improvement: if no directory is specified with the b…

    …ioruby
    
      command, use ~/.bioruby directory as the default save directory instead
      of the current directory, as suggested by Dr. Jun Sese
    ktym committed Jun 20, 2007
  2. * dir command output length ajasted

    ktym committed Jun 20, 2007
Commits on May 18, 2007
  1. * bug fix: exec_local fails to exec when @ktup is nil. This problem is

      reported and fixed by Fredrik Johansson. Thanks!
    ktym committed May 18, 2007