[BioRuby-cvs] bioruby/lib/bio/util contingency_table.rb,1.4,1.5

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory dev.open-bio.org:/tmp/cvs-serv32161

Modified Files:
	contingency_table.rb 
Log Message:
Updated license for ContingencyTable.

Index: contingency_table.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/contingency_table.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** contingency_table.rb	27 Feb 2006 13:23:01 -0000	1.4
--- contingency_table.rb	31 Dec 2006 20:02:20 -0000	1.5
***************
*** 1,11 ****
  #
! # = bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
  #
! # Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
  #
  #  $Id$
  #
! # == Synopsis
  # 
  # The Bio::ContingencyTable class provides basic statistical contingency table
--- 1,22 ----
  #
! # bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
  #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
  #
  #  $Id$
  #
! 
! module Bio #:nodoc:
! 
! #
! # bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
! #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
! #
! # = Description
  # 
  # The Bio::ContingencyTable class provides basic statistical contingency table
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*** 34,44 ****
  # 
  # 
! # == Further Reading
  # 
  # * http://en.wikipedia.org/wiki/Contingency_table
  # * http://www.physics.csbsju.edu/stats/exact.details.html
  # * Numerical Recipes in C by Press, Flannery, Teukolsky, and Vetterling
! # # 
! # == Usage
  # 
  # What follows is an example of ContingencyTable in typical usage
--- 45,55 ----
  # 
  # 
! # = Further Reading
  # 
  # * http://en.wikipedia.org/wiki/Contingency_table
  # * http://www.physics.csbsju.edu/stats/exact.details.html
  # * Numerical Recipes in C by Press, Flannery, Teukolsky, and Vetterling
! #  
! # = Usage
  # 
  # What follows is an example of ContingencyTable in typical usage
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*** 46,50 ****
  # 
  #   require 'bio'
- #   require 'bio/contingency_table'
  # 
  #   seqs = {}
--- 57,60 ----
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*** 79,85 ****
  # 
  # 
! # == Tutorial
! # 
! 
  # ContingencyTable returns the statistical significance of change
  # between two positions in an alignment.  If you would like to see how
--- 89,94 ----
  # 
  # 
! # = Tutorial
! #
  # ContingencyTable returns the statistical significance of change
  # between two positions in an alignment.  If you would like to see how
***************
*** 210,216 ****
  # 
  # 
! # == A Note on Efficiency
  # 
- 
  # ContingencyTable is slow.  It involves many calculations for even a
  # seemingly small five-string data set.  Even worse, it's very
--- 219,224 ----
  # 
  # 
! # = A Note on Efficiency
  # 
  # ContingencyTable is slow.  It involves many calculations for even a
  # seemingly small five-string data set.  Even worse, it's very
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*** 218,222 ****
  # hashes which dashes any hope of decent speed.
  # 
- 
  # Finally, half of the matrix is redundant and positions could be
  # summed with their companion position to reduce calculations.  For
--- 226,229 ----
***************
*** 230,257 ****
  # BioRuby project moves towards C extensions in the future a
  # professional caliber version will likely be created.
- # 
- # 
- #--
- #
- #  This library is free software; you can redistribute it and/or
- #  modify it under the terms of the GNU Lesser General Public
- #  License as published by the Free Software Foundation; either
- #  version 2 of the License, or (at your option) any later version.
  #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
! #
! #++
! #
! #
! 
! module Bio
! 
  class ContingencyTable
    # Since we're making this math-notation friendly here is the layout of @table:
--- 237,242 ----
  # BioRuby project moves towards C extensions in the future a
  # professional caliber version will likely be created.
  #
!   
  class ContingencyTable
    # Since we're making this math-notation friendly here is the layout of @table:
***************
*** 338,343 ****
    end
  
! end
! 
  end # Bio
  
--- 323,327 ----
    end
  
! end # ContingencyTable
  end # Bio