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|
#
# 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
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