[BioRuby-cvs] bioruby/lib/bio/util color_scheme.rb,1.2,1.3

Sun Dec 31 19:47:37 UTC 2006

Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory dev.open-bio.org:/tmp/cvs-serv32077/util

Modified Files:
	color_scheme.rb 
Log Message:
Update license for ColorScheme.

Index: color_scheme.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** color_scheme.rb	13 Dec 2005 14:58:07 -0000	1.2
--- color_scheme.rb	31 Dec 2006 19:47:35 -0000	1.3
***************
*** 1,120 ****
- module Bio
- 
  #
  # bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
  #
! # Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
  #
  #  $Id$
  #
  #
! #--
! #
! #  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
  #
! #++
  #
  #

- =begin rdoc
- bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
- 
- == Synopsis
- 
- The Bio::ColorScheme module contains classes that return popular color codings
- for nucleic and amino acids in RGB hex format suitable for HTML code.
- 
- The current schemes supported are:
- * Buried - Buried index
- * Helix - Helix propensity
- * Hydropathy - Hydrophobicity
- * Nucleotide - Nucelotide color coding
- * Strand - Strand propensity
- * Taylor - Taylor color coding
- * Turn - Turn propensity
- * Zappo - Zappo color coding
- 
- Planned color schemes include:
- * BLOSUM62
- * ClustalX
- * Percentage Identity (PID)
- 
- Color schemes BLOSUM62, ClustalX, and Percentage Identity are all dependent
- on the alignment consensus.
- 
- This data is currently referenced from the JalView alignment editor.
- Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), 
- "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
- http://www.jalview.org
- 
- Currently the score data for things such as hydropathy, helix, turn, etc. are contained
- here but should be moved to bio/data/aa once a good reference is found for these
- values.
- 
- 
- == Usage
- 
-   require 'bio/util/color_scheme'
- 
-   seq = 'gattaca'
-   scheme = Bio::ColorScheme::Zappo
-   postfix = '</span>'
-   html = ''
-   seq.each_byte do |c|
-     color = scheme[c.chr]
-     prefix = %Q(<span style="background:\##{color};">)
-     html += prefix + c.chr + postfix
-   end
- 
-   puts html
- 
- 
- === Accessing colors
- 
-   puts Bio::ColorScheme::Buried['A']  # 00DC22
-   puts Bio::ColorScheme::Buried[:c]   # 00BF3F
-   puts Bio::ColorScheme::Buried[nil]  # nil
-   puts Bio::ColorScheme::Buried['-']  # FFFFFF
-   puts Bio::ColorScheme::Buried[7]    # FFFFFF
-   puts Bio::ColorScheme::Buried['junk']  # FFFFFF
-   puts Bio::ColorScheme::Buried['t']  # 00CC32
- 
- 
- == Author
- Trevor Wennblom <trevor at corevx.com>
- 
- 
- == Copyright
- Copyright (C) 2005 Trevor Wennblom
- Licensed under the same terms as BioRuby.
- 
- =end
  module ColorScheme
!   cs_location = 'bio/util/color_scheme'

    # Score sub-classes
!   autoload :Buried, "#{cs_location}/buried"
!   autoload :Helix, "#{cs_location}/helix"
!   autoload :Hydropathy, "#{cs_location}/hydropathy"
!   autoload :Strand, "#{cs_location}/strand"
!   autoload :Turn, "#{cs_location}/turn"

    # Simple sub-classes
!   autoload :Nucleotide, "#{cs_location}/nucleotide"
!   autoload :Taylor, "#{cs_location}/taylor"
!   autoload :Zappo, "#{cs_location}/zappo"

    # Consensus sub-classes
--- 1,97 ----
  #
  # bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
  #
! # 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/color_scheme.rb - Popular color codings for nucleic and amino acids
  #
! # 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::ColorScheme module contains classes that return popular color codings
+ # for nucleic and amino acids in RGB hex format suitable for HTML code.
+ # 
+ # The current schemes supported are:
+ # * Buried - Buried index
+ # * Helix - Helix propensity
+ # * Hydropathy - Hydrophobicity
+ # * Nucleotide - Nucelotide color coding
+ # * Strand - Strand propensity
+ # * Taylor - Taylor color coding
+ # * Turn - Turn propensity
+ # * Zappo - Zappo color coding
+ # 
+ # Planned color schemes include:
+ # * BLOSUM62
+ # * ClustalX
+ # * Percentage Identity (PID)
+ # 
+ # Color schemes BLOSUM62, ClustalX, and Percentage Identity are all dependent
+ # on the alignment consensus.
+ # 
+ # This data is currently referenced from the JalView alignment editor.
+ # Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), 
+ # "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7
+ # http://www.jalview.org
+ # 
+ # Currently the score data for things such as hydropathy, helix, turn, etc. are contained
+ # here but should be moved to bio/data/aa once a good reference is found for these
+ # values.
+ # 
+ # 
+ # = Usage
+ # 
+ #   require 'bio'
+ # 
+ #   seq = 'gattaca'
+ #   scheme = Bio::ColorScheme::Zappo
+ #   postfix = '</span>'
+ #   html = ''
+ #   seq.each_byte do |c|
+ #     color = scheme[c.chr]
+ #     prefix = %Q(<span style="background:\##{color};">)
+ #     html += prefix + c.chr + postfix
+ #   end
+ # 
+ #   puts html
+ # 
+ # 
+ # == Accessing colors
+ # 
+ #   puts Bio::ColorScheme::Buried['A']  # 00DC22
+ #   puts Bio::ColorScheme::Buried[:c]   # 00BF3F
+ #   puts Bio::ColorScheme::Buried[nil]  # nil
+ #   puts Bio::ColorScheme::Buried['-']  # FFFFFF
+ #   puts Bio::ColorScheme::Buried[7]    # FFFFFF
+ #   puts Bio::ColorScheme::Buried['junk']  # FFFFFF
+ #   puts Bio::ColorScheme::Buried['t']  # 00CC32
+ # 

  module ColorScheme
!   cs_location = File.join(File.dirname(File.expand_path(__FILE__)), 'color_scheme')

    # Score sub-classes
!   autoload :Buried,     File.join(cs_location, 'buried')
!   autoload :Helix,      File.join(cs_location, 'helix')
!   autoload :Hydropathy, File.join(cs_location, 'hydropathy')
!   autoload :Strand,     File.join(cs_location, 'strand')
!   autoload :Turn,       File.join(cs_location, 'turn')

    # Simple sub-classes
!   autoload :Nucleotide, File.join(cs_location, 'nucleotide')
!   autoload :Taylor,     File.join(cs_location, 'taylor')
!   autoload :Zappo,      File.join(cs_location, 'zappo')

    # Consensus sub-classes
***************
*** 125,129 ****

    # A very basic class template for color code referencing.
!   class Simple
      def self.[](x)
        return if x.nil?
--- 102,106 ----

    # A very basic class template for color code referencing.
!   class Simple #:nodoc:
      def self.[](x)
        return if x.nil?
***************
*** 149,153 ****
    # that are score based.  This template is expected to change
    # when the scores are moved into bio/data/aa
!   class Score
      def self.[](x)
        return if x.nil?
--- 126,130 ----
    # that are score based.  This template is expected to change
    # when the scores are moved into bio/data/aa
!   class Score #:nodoc:
      def self.[](x)
        return if x.nil?
***************
*** 207,212 ****

!   # NOTE todo
!   class Consensus
    end

--- 184,189 ----

!   # TODO
!   class Consensus #:nodoc:
    end