[BioRuby-cvs] bioruby/lib/bio/appl blast.rb, 1.31, 1.32 emboss.rb, 1.6, 1.7

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv841/lib/bio/appl

Modified Files:
	blast.rb emboss.rb 
Log Message:
* minor doc fix


Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** emboss.rb	14 Jul 2006 14:28:44 -0000	1.6
--- emboss.rb	19 Sep 2006 06:31:08 -0000	1.7
***************
*** 2,25 ****
  # = bio/appl/emboss.rb - EMBOSS wrapper
  # 
! # Copyright (C):: 2002, 2005  KATAYAMA Toshiaki <k at bioruby.org>
! # Copyright (C):: 2006        Aerts Jan <jan.aerts at bbsrc.ac.uk>
! #
! # License::	Ruby's
  #
  # $Id$
  #
! # = DESCRIPTION
! #
! # This file holds classes pertaining to the EMBOSS software suite.
! #
! # = REFERENCES
! #
! # * http://emboss.sourceforge.net
! # * Rice P, Longden I and Bleasby A. \
! #    EMBOSS: the European Molecular Biology Open Software Suite. \
! #    Trends Genet. 2000 Jun ; 16(6): 276-7 
  module Bio
  
! # = DESCRIPTION
  #
  # This class provides a wrapper for the applications of the EMBOSS suite, which 
--- 2,17 ----
  # = bio/appl/emboss.rb - EMBOSS wrapper
  # 
! # Copyright::  Copyright (C) 2002, 2005 Toshiaki Katayama<k at bioruby.org>
! # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::    Ruby's
  #
  # $Id$
  #
! 
  module Bio
  
! # == Description
! #
! # This file holds classes pertaining to the EMBOSS software suite.
  #
  # This class provides a wrapper for the applications of the EMBOSS suite, which 
***************
*** 38,42 ****
  #
  #
! # = USAGE
  #
  #  require 'bio'
--- 30,34 ----
  #
  #
! # == Usage
  #
  #  require 'bio'
***************
*** 61,70 ****
  #  puts Bio::EMBOSS.entret('embl:xlrhodop')
  #
! # = PREREQUISITES
  #
  # You must have the EMBOSS suite installed locally. You can download from the
  # project website (see References below).
  #
! # = REFERENCES
  #
  # * http://emboss.sourceforge.net
--- 53,62 ----
  #  puts Bio::EMBOSS.entret('embl:xlrhodop')
  #
! # == Pre-requisites
  #
  # You must have the EMBOSS suite installed locally. You can download from the
  # project website (see References below).
  #
! # = Rereferences
  #
  # * http://emboss.sourceforge.net
***************
*** 72,75 ****
--- 64,68 ----
  #    EMBOSS: the European Molecular Biology Open Software Suite. \
  #    Trends Genet. 2000 Jun ; 16(6): 276-7 
+ #
  class EMBOSS
  

Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** blast.rb	25 Jul 2006 18:47:13 -0000	1.31
--- blast.rb	19 Sep 2006 06:31:08 -0000	1.32
***************
*** 2,22 ****
  # = bio/appl/blast.rb - BLAST wrapper
  # 
! # Copyright (C)::  2001       Mitsuteru C. Nakao <n at bioruby.org>
! # Copyright (C)::  2002,2003  KATAYAMA Toshiaki <k at bioruby.org>
! # Copyright (C)::  2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! #
  # License::    Ruby's
  #
  # $Id$
  #
- # = DESCRIPTION
- #
- # This file holds the Bio::Blast class, which creates BLAST factories.
- #
- # = References
- #
- # * http://www.ncbi.nlm.nih.gov/blast/
- # * http://blast.genome.jp/ideas/ideas.html#blast
- #
  
  require 'net/http'
--- 2,12 ----
  # = bio/appl/blast.rb - BLAST wrapper
  # 
! # Copyright::  Copyright (C) 2001       Mitsuteru C. Nakao <n at bioruby.org>
! # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
! # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::    Ruby's
  #
  # $Id$
  #
  
  require 'net/http'
***************
*** 27,31 ****
  module Bio
  
!   # = DESCRIPTION
    # 
    # The Bio::Blast class contains methods for running local or remote BLAST
--- 17,21 ----
  module Bio
  
!   # == Description
    # 
    # The Bio::Blast class contains methods for running local or remote BLAST
***************
*** 34,38 ****
    # program, see http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html.
    #
!   # = USAGE
    #
    #   require 'bio'
--- 24,28 ----
    # program, see http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html.
    #
!   # == Usage
    #
    #   require 'bio'
***************
*** 50,54 ****
    #   # Then, to parse the report, see Bio::Blast::Report
    #
!   # == Available databases for Bio::Blast.remote
    #
    #  ----------+-------+---------------------------------------------------
--- 40,44 ----
    #   # Then, to parse the report, see Bio::Blast::Report
    #
!   # === Available databases for Bio::Blast.remote
    #
    #  ----------+-------+---------------------------------------------------
***************
*** 64,68 ****
    #  ----------+-------+---------------------------------------------------
    #
!   # = SEE ALSO
    #
    # * Bio::Blast::Report
--- 54,58 ----
    #  ----------+-------+---------------------------------------------------
    #
!   # == See also
    #
    # * Bio::Blast::Report
***************
*** 70,75 ****
    # * Bio::Blast::Report::Hsp
    #
!   # = REFERENCE
    # 
    # * http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html
    # * http://blast.genome.jp/ideas/ideas.html#blast
--- 60,66 ----
    # * Bio::Blast::Report::Hsp
    #
!   # == References
    # 
+   # * http://www.ncbi.nlm.nih.gov/blast/
    # * http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html
    # * http://blast.genome.jp/ideas/ideas.html#blast