[BioRuby-cvs] bioruby/lib/bio/db aaindex.rb,1.13,1.14

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv17322/lib/bio/db

Modified Files:
	aaindex.rb 
Log Message:
* Converted to RDoc.


Index: aaindex.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/aaindex.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** aaindex.rb	8 Sep 2005 01:22:11 -0000	1.13
--- aaindex.rb	7 Nov 2005 10:14:28 -0000	1.14
***************
*** 1,6 ****
  #
! # bio/db/aaindex.rb - AAindex database class
  #
! #   Copyright (C) 2001 KAWASHIMA Shuichi <s at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,16 ----
  #
! # = bio/db/aaindex.rb - AAindex database class
  #
! # Copyright::  Copyright (C) 2001 KAWASHIMA Shuichi <s at bioruby.org>
! # Licence::    LGPL
! #
! #  $Id$
! #
! # == Description
! #
! #
! # == Example
! # == References
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
--- 28,32 ----
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
  
***************
*** 28,62 ****
    class AAindex < KEGGDB
  
!     DELIMITER	= RS = "\n//\n"
      TAGSIZE	= 2
  
      def initialize(entry)
        super(entry, TAGSIZE)
      end
  
      def entry_id
        field_fetch('H')
      end
  
      def definition
        field_fetch('D')
      end
  
      def dblinks
        field_fetch('R')
      end
  
      def author
        field_fetch('A')
      end
  
      def title
        field_fetch('T')
      end
  
      def journal
        field_fetch('J')
      end
  
      def comment
        get('*')
--- 38,86 ----
    class AAindex < KEGGDB
  
!     # Delimiter
!     DELIMITER	="\n//\n"
! 
!     # Delimiter
!     RS = DELIMITER
! 
!     #
      TAGSIZE	= 2
  
+     #
      def initialize(entry)
        super(entry, TAGSIZE)
      end
  
+     # Returns
      def entry_id
        field_fetch('H')
      end
  
+     # Returns
      def definition
        field_fetch('D')
      end
  
+     # Returns
      def dblinks
        field_fetch('R')
      end
  
+     # Returns
      def author
        field_fetch('A')
      end
  
+     # Returns
      def title
        field_fetch('T')
      end
  
+     # Returns
      def journal
        field_fetch('J')
      end
  
+     # Returns
      def comment
        get('*')
***************
*** 68,79 ****
--- 92,106 ----
    class AAindex1 < AAindex
  
+     #
      def initialize(entry)
        super(entry)
      end
  
+     # Returns
      def correlation_coefficient
        field_fetch('C')
      end
  
+     # Returns
      def index(type = :float)
        aa = %w( A R N D C Q E G H I L K M F P S T W Y V )
***************
*** 126,133 ****
--- 153,162 ----
    class AAindex2 < AAindex
  
+     #
      def initialize(entry)
        super(entry)
      end
  
+     # Returns
      def rows
        label_data
***************
*** 135,138 ****
--- 164,168 ----
      end
  
+     # Returns
      def cols
        label_data
***************
*** 140,143 ****
--- 170,174 ----
      end
  
+     # Returns
      def matrix
        ma = Array.new
***************
*** 152,155 ****
--- 183,187 ----
      end
  
+     # Returns
      def old_matrix	# for AAindex <= ver 5.0
  
***************
*** 234,262 ****
    p aax2.matrix.transpose
  end
- 
- =begin
- 
- = Bio::AAindex
- 
- --- Bio::AAindex.new(entry)
- --- Bio::AAindex#entry_id
- --- Bio::AAindex#definition
- --- Bio::AAindex#dblinks
- --- Bio::AAindex#author
- --- Bio::AAindex#title
- --- Bio::AAindex#journal
- --- Bio::AAindex#comment
- 
- = Bio::AAindex1
- 
- --- Bio::AAindex1#correlation_coefficient
- --- Bio::AAindex1#index
- 
- = Bio::AAindex2
- 
- --- Bio::AAindex2#matrix
- --- Bio::AAindex2#rows
- --- Bio::AAindex2#cols
- 
- =end
  
--- 266,268 ----