[BioRuby-cvs] bioruby/lib/bio/appl/mafft report.rb,1.5,1.6

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft
In directory pub.open-bio.org:/tmp/cvs-serv32324/mafft

Modified Files:
	report.rb 
Log Message:
Changed document format from RD to RDoc.
Added references to the document.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb	26 Sep 2005 13:00:05 -0000	1.5
--- report.rb	31 Oct 2005 12:47:12 -0000	1.6
***************
*** 1,7 ****
  #
! # bio/appl/mafft/report.rb - MAFFT report class
  #
! #   Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
  #
  #  This library is free software; you can redistribute it and/or
  #  modify it under the terms of the GNU Lesser General Public
--- 1,9 ----
  #
! # = bio/appl/mafft/report.rb - MAFFT report class
  #
! # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # Licence::   LGPL
  #
+ #--
  #  This library is free software; you can redistribute it and/or
  #  modify it under the terms of the GNU Lesser General Public
***************
*** 17,23 ****
--- 19,41 ----
  #  License along with this library; if not, write to the Free Software
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+ #++
  #
  #  $Id$
  #
+ # MAFFT result parser class.
+ # MAFFT is a very fast multiple sequence alignment software.
+ #
+ # Since a result of MAFFT is simply a multiple-fasta format,
+ # the significance of this class is to keep standard form and
+ # interface between Bio::ClustalW::Report.
+ #
+ # == References
+ #
+ # * K. Katoh, K. Misawa, K. Kuma and T. Miyata.
+ #   MAFFT: a novel method for rapid multiple sequence alignment based
+ #   on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066, 2002.
+ #   http://nar.oupjournals.org/cgi/content/abstract/30/14/3059
+ # * http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
+ #
  
  require 'bio/db/fasta'
***************
*** 25,32 ****
  require 'bio/appl/mafft'
  
! module Bio
!   class MAFFT
      class Report
  
        def initialize(ary, seqclass = nil)
          @data = ary
--- 43,62 ----
  require 'bio/appl/mafft'
  
! module Bio #:nodoc:
!   class MAFFT #:nodoc:
! 
!     # MAFFT result parser class.
!     # MAFFT is a very fast multiple sequence alignment software.
!     #
!     # Since a result of MAFFT is simply a multiple-fasta format,
!     # the significance of this class is to keep standard form and
!     # interface between Bio::ClustalW::Report.
      class Report
  
+       # Creates a new Report object.
+       # +ary+ should be an Array of Bio::FastaFormat.
+       # +seqclass+ should on of following:
+       # Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
+       # String: 'PROTEIN', 'DNA', ...
        def initialize(ary, seqclass = nil)
          @data = ary
***************
*** 45,51 ****
--- 75,87 ----
          end
        end
+ 
+       # sequence data. Returns an array of Bio::FastaFormat.
        attr_reader :data
+ 
+       # Sequence class (Bio::Sequence::AA, Bio::Sequence::NA, ...)
        attr_reader :seqclass
  
+       # Gets an multiple alignment.
+       # Returns an instance of Bio::Alignment class.
        def align
          do_parse() unless @align
***************
*** 54,61 ****
--- 90,103 ----
        alias alignment align
  
+       # Gets an fasta-format string of the sequences.
+       # Returns a string.
+       # Same as align.to_fasta.
+       # Please refer to Bio::Alignment#to_fasta for arguments.
        def to_fasta(*arg)
          align.to_fasta(*arg)
        end
  
+       # Gets an array of the sequences.
+       # Returns an array of Bio::FastaFormat instances.
        def to_a
          @data
***************
*** 63,66 ****
--- 105,109 ----
  
        private
+       # Parsing a result.
        def do_parse
          return nil if @align
***************
*** 75,115 ****
  end #module Bio
  
- =begin
- 
- = Bio::MAFFT::Report
- 
-     MAFFT result parser class.
-     Since a result of MAFFT is simply a multiple-fasta format,
-     the significance of this class is to keep standard form and
-     interface between Bio::ClustalW::Report.
- 
- --- Bio::MAFFT::Report.new(data, seqclass = nil)
- 
-     Creates new instance.
-     'data' should be an Array of Bio::FastaFormat.
-     'seqclass' should on of following:
-       Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
-       String: 'PROTEIN', 'DNA', ...
- 
- --- Bio::MAFFT::Report#data
- --- Bio::MAFFT::Report#seqclass
- 
-     Acess methods of variables given in Bio::MAFFT::Report.new method.
- 
- --- Bio::MAFFT::Report#alginment
- --- Bio::MAFFT::Report#algin
- 
-     Gets an multiple alignment.
-     Returns an instance of Bio::Alignment class.
- 
- --- Bio::MAFFT::Report#to_a
- 
-     Gets an array of the sequences.
-     Returns an array of Bio::FastaFormat instances.
- 
- --- Bio::MAFFT::Report#to_fasta
- 
-     Gets an fasta-format string of the sequences.
-     Returns a string.
- 
- =end
--- 118,119 ----