Permalink
Commits on Aug 9, 2005
  1. * prepared for 0.6.3 release

    ktym committed Aug 9, 2005
  2. * bug fixed by Masashi Fujita (2005/5/26) -- sometimes sequence position

    ktym committed Aug 9, 2005
      in HMMER report becomes '-' instead of digits according to the alignment.
  3. * each_entry: changed to return self

    ngoto committed Aug 9, 2005
    * changes in 1.2 -> 1.3 (sorry, I forgot to write)
      * using thread to read stderr
  4. * Changed not to execute shell when execute command

    ngoto committed Aug 9, 2005
    * Using block with Open3.popen3
    * removed rescue
  5. * added sirna, fastacmd

    ktym committed Aug 9, 2005
  6. * the class is renamed to Bio::Fastacmd (from Bio::BlastDB)

    ktym committed Aug 9, 2005
    * constant FASTACMD is changed to an instance variable
    * added accessors for database and fastacmd
    * get_by_ids method is integrated into fetch method
    * test code modified to accept arguments
  7. * removed redundancy

    ktym committed Aug 9, 2005
  8. * clean up by katayama

    ktym committed Aug 9, 2005
Commits on Aug 8, 2005
  1. * Added Bio::SPTR#protein_name method (proposed by Luca Pireddu).

    nakao committed Aug 8, 2005
    * Added Bio::SPTR#synomyms method (proposed by Luca Pireddu).
    * Changed Bio::SPTR#gn to parsing newly GN line format (proposed by Luca
      Pireddu).
    * Changed Bio::SPTR#gene_names method (proposed by Luca Pireddu).
    * Changed Bio::SPTR#gene_name method (proposed by Luca Pireddu).
Commits on Aug 7, 2005
  1. * AminoAcid#to_re method is added

    ktym committed Aug 7, 2005
    * clean up
  2. added Changelog for lib/bio/appl/bl2seq/report.rb and

    ngoto committed Aug 7, 2005
    lib/bio/appl/blast/format0.rb
  3. * lib/bio/appl/bl2seq/report.rb:

    ngoto committed Aug 7, 2005
      Newly added bl2seq (BLAST 2 sequences) output parser.
    * lib/bio/appl/blast/format0.rb:
      Added `self.class::` before F0dbstat.new for bl2seq/report.rb
  4. * entry string is changed to be stripped before passed to entry2hash …

    ktym committed Aug 7, 2005
    …method
    
      in initialize
  5. * prepared for 0.6.3

    ktym committed Aug 7, 2005
  6. * Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have Dat…

    ktym committed Aug 7, 2005
    …a module
    
      and this module is included and extended to make methods as both of
      instance methods and extend methods
    * Bio::Sequence::NA class is rewrited (molecular_weight, to_re methods)
      to use Bio::NucleicAcid
    * molecular_weight method is fixed to subtract two hydrogens for each base
  7. * Re-formated codes.

    nakao committed Aug 7, 2005
  8. Avoid NoMethodError (private method `chomp` called for nil:NilClass)

    ngoto committed Aug 7, 2005
    when parsing features of
    ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
    Salmonella_typhimurium_LT2/AE006468.gbk
Commits on Jul 11, 2005
  1. * added higet

    ktym committed Jul 11, 2005
    * prepared for 0.6.3
  2. * added higet

    ktym committed Jul 11, 2005