[BioRuby-cvs] bioruby/lib/bio/db aaindex.rb, 1.15, 1.16 gff.rb, 1.4, 1.5 litdb.rb, 0.6, 0.7 nbrf.rb, 1.6, 1.7

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv28824/db

Modified Files:
	aaindex.rb gff.rb litdb.rb nbrf.rb 
Log Message:
* s/Licence/License/


Index: litdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/litdb.rb,v
retrieving revision 0.6
retrieving revision 0.7
diff -C2 -d -r0.6 -r0.7
*** litdb.rb	7 Nov 2005 14:28:12 -0000	0.6
--- litdb.rb	18 Dec 2005 15:58:41 -0000	0.7
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2001 KATAYAMA Toshiaki <k at bioruby.org>
! # Licence::    LGPL
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2001 KATAYAMA Toshiaki <k at bioruby.org>
! # License::    LGPL
  #
  #  $Id$

Index: aaindex.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/aaindex.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** aaindex.rb	8 Nov 2005 02:13:44 -0000	1.15
--- aaindex.rb	18 Dec 2005 15:58:41 -0000	1.16
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2001 KAWASHIMA Shuichi <s at bioruby.org>
! # Licence::    LGPL
  #
  # $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2001 KAWASHIMA Shuichi <s at bioruby.org>
! # License::    LGPL
  #
  # $Id$

Index: nbrf.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** nbrf.rb	1 Nov 2005 05:32:24 -0000	1.6
--- nbrf.rb	18 Dec 2005 15:58:41 -0000	1.7
***************
*** 4,8 ****
  # Copyright:: Copyright (C) 2001-2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #             Copyright (C) 2001-2002 KATAYAMA Toshiaki <k at bioruby.org>
! # Licence::   LGPL
  #
  #--
--- 4,8 ----
  # Copyright:: Copyright (C) 2001-2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #             Copyright (C) 2001-2002 KATAYAMA Toshiaki <k at bioruby.org>
! # License::   LGPL
  #
  #--

Index: gff.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/gff.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** gff.rb	7 Nov 2005 13:19:17 -0000	1.4
--- gff.rb	18 Dec 2005 15:58:41 -0000	1.5
***************
*** 2,9 ****
  # = bio/db/gff.rb - GFF format class
  #
! # Copyright::  Copyright (C) 2003 KATAYAMA Toshiaki <k at bioruby.org>
! # Licence::    LGPL
  #
! #  $Id$
  #
  # == Description
--- 2,10 ----
  # = bio/db/gff.rb - GFF format class
  #
! # Copyright::  Copyright (C) 2003, 2005
! #              Toshiaki Katayama <k at bioruby.org>
! # License::    LGPL
  #
! # $Id$
  #
  # == Description
***************
*** 11,15 ****
--- 12,19 ----
  #
  # == Example
+ #
+ #
  # == References
+ #
  # * http://www.sanger.ac.uk/Software/formats/GFF/
  #
***************
*** 35,122 ****
  module Bio
  
!   # = GFF
!   class GFF
  
!     # Returns
!     attr_accessor :records
  
!     #
!     def initialize(str = '')
!       @records = Array.new
!       str.each_line do |line|
!         @records << Record.new(line)
!       end
      end
  
!     # = GFF::Record
!     class Record
! 
!       # Returns
!       attr_accessor :seqname
! 
!       # Returns
!       attr_accessor :source
! 
!       # Returns
!       attr_accessor :feature
! 
!       # Returns
!       attr_accessor :start
! 
!       # Returns
!       attr_accessor :end
! 
!       # Returns
!       attr_accessor :score
! 
!       # Returns
!       attr_accessor :strand
! 
!       # Returns
!       attr_accessor :frame
! 
!       # Returns
!       attr_accessor :attributes
  
!       # Returns
!       attr_accessor :comments
  
!       #
!       def initialize(str)
!         @comments = str.chomp[/#.*/]
!         return if /^#/.match(str)
!         @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
!           attributes, = str.chomp.split("\t")
!         @attributes = parse_attributes(attributes) if attributes
!       end
  
!       private
  
!       def parse_attributes(attributes)
!         hash = Hash.new
!         attributes.split(/[^\\];/).each do |atr|
!           key, value = atr.split(' ', 2)
!           hash[key] = value
!         end
!         return hash
        end
      end
    end
  
-   # = GFF2
    class GFF2 < GFF
- 
-     #
      VERSION = 2
    end
  
-   # = GFF3
    class GFF3 < GFF
- 
-     #
      VERSION = 3
    end
  
! end
  
  
--- 39,97 ----
  module Bio
  
! class GFF
  
!   attr_accessor :records
  
!   def initialize(str = '')
!     @records = Array.new
!     str.each_line do |line|
!       @records << Record.new(line)
      end
+   end
  
!   class Record
  
!     attr_accessor :seqname
!     attr_accessor :source
!     attr_accessor :feature
!     attr_accessor :start
!     attr_accessor :end
!     attr_accessor :score
!     attr_accessor :strand
!     attr_accessor :frame
!     attr_accessor :attributes
!     attr_accessor :comments
  
!     def initialize(str)
!       @comments = str.chomp[/#.*/]
!       return if /^#/.match(str)
!       @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
!         attributes, = str.chomp.split("\t")
!       @attributes = parse_attributes(attributes) if attributes
!     end
  
!     private
  
!     def parse_attributes(attributes)
!       hash = Hash.new
!       attributes.split(/[^\\];/).each do |atr|
!         key, value = atr.split(' ', 2)
!         hash[key] = value
        end
+       return hash
      end
    end
  
    class GFF2 < GFF
      VERSION = 2
    end
  
    class GFF3 < GFF
      VERSION = 3
    end
  
! end # class GFF
! 
! end # module Bio