#
# bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
#
# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License::   The Ruby License
#
#  $Id:$
#

module Bio

#
# bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
#
# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License::   The Ruby License
#
#
# = 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
  # NOTE todo
  # BLOSUM62
  # ClustalX
  # PID

  # A very basic class template for color code referencing.
  class Simple #:nodoc:
    def self.[](x)
      return if x.nil?
      # accept symbols and any case
      @colors[x.to_s.upcase]
    end

    def self.colors() @colors end

    #######
    private
    #######

    # Example
    @colors = {
      'A' => '64F73F',
    }
    @colors.default = 'FFFFFF'  # return white by default
  end


  # A class template for color code referencing of color schemes
  # 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?
      # accept symbols and any case
      @colors[x.to_s.upcase]
    end

    def self.min(x) @min end
    def self.max(x) @max end
    def self.scores() @scores end
    def self.colors() @colors end

    #########
    protected
    #########

    def self.percent_to_hex(percent)
      percent = percent.to_f if percent.is_a?(String)
      if (percent > 1.0) or (percent < 0.0) or percent.nil?
        raise 'Percentage must be between 0.0 and 1.0'
      end
      "%02X" % (percent * 255.0)
    end

    def self.rgb_percent_to_hex(red, green, blue)
      percent_to_hex(red) + percent_to_hex(green) + percent_to_hex(blue)
    end

    def self.score_to_percent(score, min, max)
      # .to_f to ensure every operation is float-aware
      percent = (score.to_f - min) / (max.to_f - min)
      percent = 1.0 if percent > 1.0
      percent = 0.0 if percent < 0.0
      percent
    end

    #######
    private
    #######

    # Example
    def self.score_to_rgb_hex(score, min, max)
      percent = score_to_percent(score, min, max)
      rgb_percent_to_hex(percent, 0.0, 1.0-percent)
    end

    @colors = {}
    @scores = {
      'A' => 0.83,
    }
    @min = 0.37
    @max = 1.7
    @scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
    @colors.default = 'FFFFFF'  # return white by default

  end


  # TODO
  class Consensus #:nodoc:
  end

end  # module ColorScheme
end  # module Bio