[BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.6,1.7

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory pub.open-bio.org:/tmp/cvs-serv32559

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/clustalw/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb	26 Sep 2005 13:00:05 -0000	1.6
--- report.rb	31 Oct 2005 13:56:09 -0000	1.7
***************
*** 1,7 ****
  #
! # bio/appl/clustalw/report.rb - CLUSTAL W format data (*.aln) 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/clustalw/report.rb - CLUSTAL W format data (*.aln) 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 ****
--- 19,39 ----
  #  License along with this library; if not, write to the Free Software
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+ #++
  #
  #  $Id$
  #
+ # Bio::ClustalW::Report is a CLUSTAL W report (*.aln file) parser.
+ # CLUSTAL W is a very popular software for multiple sequence alignment.
+ #
+ # == References
+ #
+ # * Thompson,J.D., Higgins,D.G. and Gibson,T.J..
+ #   CLUSTAL W: improving the sensitivity of progressive multiple sequence
+ #   alignment through sequence weighting, position-specific gap penalties
+ #   and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
+ #   http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673
+ # * http://www.ebi.ac.uk/clustalw/
+ # * ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+ #
  
  require 'bio/sequence'
***************
*** 26,34 ****
  require 'bio/appl/clustalw'
  
! module Bio
!   class ClustalW
      class Report < Bio::DB
        DELIMITER = nil
  
        def initialize(str, seqclass = nil)
          @raw = str
--- 42,60 ----
  require 'bio/appl/clustalw'
  
! module Bio #:nodoc:
!   class ClustalW #:nodoc:
! 
!     # CLUSTAL W result data (*.aln file) parser class.
      class Report < Bio::DB
+ 
+       # Delimiter of each entry. Bio::FlatFile uses it.
+       # In Bio::ClustalW::Report, it it nil (1 entry 1 file).
        DELIMITER = nil
  
+       # Creates new instance.
+       # +str+ should be a CLUSTAL format string.
+       # +seqclass+ should on of following:
+       # * Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
+       # * String: 'PROTEIN', 'DNA', ...
        def initialize(str, seqclass = nil)
          @raw = str
***************
*** 49,63 ****
--- 75,101 ----
          end
        end
+       # string of whole result
        attr_reader :raw
+ 
+       # sequence class (one of Bio::Sequence, Bio::Sequence::NA,
+       # Bio::Sequence::AA, ...)
        attr_reader :seqclass
  
+       # Shows first line of the result data, for example,
+       # 'CLUSTAL W (1.82) multiple sequence alignment'.
+       # Returns a string.
        def header
          @header or (do_parse or @header)
        end
  
+       # Shows "match line" of CLUSTAL's alignment result, for example,
+       # ':* :* .*   *       .*::*.   ** :* . *    .        '.
+       # Returns a string.
        def match_line
          @match_line or (do_parse or @match_line)
        end
  
+       # Gets an multiple alignment.
+       # Returns a Bio::Alignment object.
        def align
          do_parse() unless @align
***************
*** 66,73 ****
--- 104,115 ----
        alias alignment align
  
+       # Gets an fasta-format string of the sequences.
+       # Returns a string.
        def to_fasta(*arg)
          align.to_fasta(*arg)
        end
  
+       # Gets an array of the sequences.
+       # Returns an array of Bio::FastaFormat objects.
        def to_a
          align.to_fastaformat_array
***************
*** 75,78 ****
--- 117,121 ----
  
        private
+       # Parses Clustal W result text.
        def do_parse
          return nil if @align
***************
*** 110,159 ****
  end #module Bio
  
- =begin
- 
- = Bio::ClustalW::Report
- 
-  CLUSTAL W result data (*.aln file) parser class.
- 
- --- Bio::ClustalW::Report.new(raw, seqclass = nil)
- 
-     Creates new instance.
-     'raw' should be a string of CLUSTAL format data.
-     'seqclass' should on of following:
-       Class:  Bio::Sequence::AA, Bio::Sequence::NA, ...
-       String: 'PROTEIN', 'DNA', ...
- 
- --- Bio::ClustalW::Report#raw
- --- Bio::ClustalW::Report#seqclass
- 
-     Acess methods of variables given in Bio::ClustalW::Report.new method.
- 
- --- Bio::ClustalW::Report#alginment
- --- Bio::ClustalW::Report#algin
- 
-     Gets an multiple alignment.
-     Returns an instance of Bio::Alignment class.
- 
- --- Bio::ClustalW::Report#to_a
- 
-     Gets an array of the sequences.
-     Returns an array of Bio::FastaFormat instances.
- 
- --- Bio::ClustalW::Report#to_fasta
- 
-     Gets an fasta-format string of the sequences.
-     Returns a string.
- 
- --- Bio::ClustalW::Report#header
- 
-     Shows first line of the result data, for example,
-         'CLUSTAL W (1.82) multiple sequence alignment'.
-     Returns a string.
- 
- --- Bio::ClustalW::Report#match_line
- 
-     Shows "match line" of CLUSTAL's alignment result, for example,
-         ':* :* .*   *       .*::*.   ** :* . *    .        '.
-     Returns a string.
- 
- =end
--- 153,154 ----