Skip to content
This repository

Aug 09, 2005

  1. ktym

    * added sirna.rb and fastacmd.rb

    authored August 09, 2005
  2. ktym

    * FTP removed... (many other points are also needed to be fixed)

    authored August 09, 2005
  3. ktym

    * prepared for 0.6.3 release

    authored August 09, 2005
  4. Mitsuteru Nakao

    * added log for lib/bio/db/embl/sptr.rb.

    authored August 09, 2005
  5. ktym

    * bug fixed by Masashi Fujita (2005/5/26) -- sometimes sequence position

      in HMMER report becomes '-' instead of digits according to the alignment.
    authored August 09, 2005
  6. Naohisa Goto

    * each_entry: changed to return self

    * changes in 1.2 -> 1.3 (sorry, I forgot to write)
      * using thread to read stderr
    authored August 09, 2005
  7. Naohisa Goto

    * Changed not to execute shell when execute command

    * Using block with Open3.popen3
    * removed rescue
    authored August 09, 2005
  8. ktym

    * added sirna, fastacmd

    authored August 09, 2005
  9. ktym

    * the class is renamed to Bio::Fastacmd (from Bio::BlastDB)

    * 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
    authored August 09, 2005
  10. ktym

    * Contributed by Shuji SHIGENOBU <shige@nibb.ac.jp>

    authored August 09, 2005
  11. ktym

    * removed redundancy

    authored August 09, 2005
  12. ktym

    * clean up by katayama

    authored August 09, 2005
  13. ktym

    * Contributed by Itoshi Nikaido <dritoshi@gmail.com>

    authored August 09, 2005

Aug 08, 2005

  1. ktym

    * weight of hydrogen is changed to precise value

    authored August 08, 2005
  2. Mitsuteru Nakao

    * Added Bio::SPTR#protein_name method (proposed by Luca Pireddu).

    * 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).
    authored August 08, 2005
  3. ktym

    * Bio::Sequence::AA#to_re is changed to use AminoAcid.to_re

    authored August 08, 2005

Aug 07, 2005

  1. ktym

    * AminoAcid#to_re method is added

    * clean up
    authored August 07, 2005
  2. Naohisa Goto

    added Changelog for lib/bio/appl/bl2seq/report.rb and

    lib/bio/appl/blast/format0.rb
    authored August 07, 2005
  3. Naohisa Goto

    * lib/bio/appl/bl2seq/report.rb:

      Newly added bl2seq (BLAST 2 sequences) output parser.
    * lib/bio/appl/blast/format0.rb:
      Added `self.class::` before F0dbstat.new for bl2seq/report.rb
    authored August 07, 2005
  4. ktym

    * bget method is fixed to surely confirm that the returned value exists.

    authored August 07, 2005
  5. ktym

    * fixed Bio::Sequence::AA#molecular_weight to use AminoAcid#weight also

    authored August 07, 2005
  6. ktym

    * fixed to avoid adding nil to string

    authored August 07, 2005
  7. ktym

    * entry string is changed to be stripped before passed to entry2hash …

    …method
    
      in initialize
    authored August 07, 2005
  8. ktym

    * entry_id method is fixed to return the first word in the ENTRY line

    authored August 07, 2005
  9. ktym

    * prepared for 0.6.3

    authored August 07, 2005
  10. ktym

    * Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have Dat…

    …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
    authored August 07, 2005
  11. ktym

    * publication_type method is added

    authored August 07, 2005
  12. Mitsuteru Nakao

    * Re-formated codes.

    authored August 07, 2005
  13. Naohisa Goto

    added log for lib/bio/db/genbank/common.rb modified today

    authored August 07, 2005
  14. Naohisa Goto

    Avoid NoMethodError (private method `chomp` called for nil:NilClass)

    when parsing features of
    ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
    Salmonella_typhimurium_LT2/AE006468.gbk
    authored August 07, 2005
  15. Naohisa Goto

    added old Changelog modified by ngoto

    authored August 07, 2005

Jul 11, 2005

  1. ktym

    * added higet

    * prepared for 0.6.3
    authored July 11, 2005
  2. ktym

    * added higet

    authored July 11, 2005
  3. ktym

    * --sort page option is now available

    authored July 11, 2005
  4. ktym

    * Newly added SOAP interface for HGC HiGet service

    authored July 11, 2005
Something went wrong with that request. Please try again.