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Commits on Jul 12, 2001
  1. Initial import.

    Yoshinori Okuji committed Jul 12, 2001
  2. Initial revision

    Yoshinori Okuji committed Jul 12, 2001
Commits on Jul 5, 2001
  1. @ktym

    * 2001/07/05

    * fix - some organism names of the ORGANISM field are longer than one
            line!! (e.g. gb:AF290439)
    ktym committed Jul 5, 2001
Commits on Jun 26, 2001
  1. @ktym

    * 2001/06/26 add comment method

    ktym committed Jun 26, 2001
Commits on Jun 25, 2001
  1. @ktym

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    ktym committed Jun 25, 2001
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    ktym committed Jun 25, 2001
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    ktym committed Jun 25, 2001
  4. @ktym

    * 2001/06/25 add comment method

    ktym committed Jun 25, 2001
Commits on Jun 21, 2001
  1. @ktym

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    ktym committed Jun 21, 2001
  2. @ktym

    Initial revision

    ktym committed Jun 21, 2001
  3. @ktym

    * 2001/06/21

    * completely rewrited to use db.rb
    * profile and pdoc parser are still awaited
    ktym committed Jun 21, 2001
  4. @ktym

    * 2001/06/21 fix - EMBLDB

    ktym committed Jun 21, 2001
  5. @ktym

    * 2001/03/08

    * remove count method because superclass String already has.
    * remove to_list_long method
      * use to_list both in NAseq, AAseq
      * use to_3 when need 3 letter abbreviation
    * simplify subseq method
    ktym committed Jun 21, 2001
  6. @ktym

    * 2001/01/29 change class to module

    ktym committed Jun 21, 2001
  7. @ktym

    * 2001/01/29 rewrite

    ktym committed Jun 21, 2001
  8. @ktym

    * 2000/11/20 initial version

    * 2000/11/24 clean up & rewrite
    ktym committed Jun 21, 2001
  9. @ktym

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    ktym committed Jun 21, 2001
  10. @ktym

    * 2001/02/17 initial version created (separated from sequence.rb)

    * 2001/06/21 minor change (now CT became Hash not Array)
    ktym committed Jun 21, 2001
  11. @ktym

    * 2001/02/17 initial version created (separated from sequence.rb)

    * 2001/06/21 minor change
    ktym committed Jun 21, 2001
  12. @ktym

    * 2001/06/20 initial release version

    * 2001/06/21 fix - /#{species}/
    ktym committed Jun 21, 2001
  13. @ktym

    * 2001/06/20 initial release version

    * 2001/06/21 add to_i or to_f to statistics
    ktym committed Jun 21, 2001
  14. @ktym

    * 2001/06/21

    * completely rewrited to use db.rb
      * rename/add/delete some methods to satisfy the API of db.rb
    ktym committed Jun 21, 2001
  15. @ktym

    *** empty log message ***

    ktym committed Jun 21, 2001
  16. @ktym

    * 2001/06/21

    * completely rewrited to use db.rb
      * rename some methods to satisfy the API of db.rb
      * add some methods
      * delete some methods
      * delete short name aliases (gb.l, gb.f etc.)
    * add new LOCATION format support (from GenBank 126.0, currently 123.0)
    * FEATURE parser now use array of qualifier effectively before parsing
    ktym committed Jun 21, 2001
Commits on Jun 20, 2001
  1. @ktym

    *** empty log message ***

    ktym committed Jun 20, 2001
  2. @ktym

    * 2001/02/21 initial release version

    * 2001/03/08 add argument to id method
    ktym committed Jun 20, 2001
  3. @ktym

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    ktym committed Jun 20, 2001
  4. @ktym

    * 2001/03/08

    * add id method
    * remove alias naseq, nt
    ktym committed Jun 20, 2001
  5. @ktym

    * 2001/03/05

    * returns codon_usage as 64 dimension Array
    * change else if block_given? to elsif block_given?
    ktym committed Jun 20, 2001
  6. @ktym

    * 2001/02/21

    * add next if line =~ /^$/ (consistent with genbank.rb)
    ktym committed Jun 20, 2001
  7. @ktym

    * 2001/02/19

    * GENES::DELIMITER, GENES::TAGSIZE
    * bug fix that position(), entry() fail when missing tags
    ktym committed Jun 20, 2001
  8. @ktym

    * 2001/02/14 initial released version

    * 2001/02/15 delete all spaces in position
    ktym committed Jun 20, 2001
  9. @ktym

    *** empty log message ***

    ktym committed Jun 20, 2001
  10. @ktym

    * 2001/03/08

    * returns array of multiple db_xref in feature
    * returns codon_start in feature as to_i
    * returns true when /virion etc. exists
    * id method
    * remove alias nt
    * not specifically returns @orig because initialize seems to return
      self by default
    ktym committed Jun 20, 2001
  11. @ktym

    * 2001/03/06

    * add require 'bio/db/gblocation'
    * change regexp to match feature position
      * to rescue rare case that some entry contains space in position
        -      if line =~ /^ {5}(\S+)\s+(\S+)/
        +      if line =~ /^ {5}(\S+)\s+(.*)/
    ktym committed Jun 20, 2001
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