jandot-bio 1.2.1

data/lib/bio/util/color_scheme.rb

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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: color_scheme.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+#
+
+module Bio #:nodoc:
+
+#
+# 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

data/lib/bio/util/color_scheme/buried.rb

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+#
+# bio/util/color_scheme/buried.rb - Color codings for buried 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: buried.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+  class Buried < Score #:nodoc:
+
+    #########
+    protected
+    #########
+
+    def self.score_to_rgb_hex(score, min, max)
+      percent = score_to_percent(score, min, max)
+      rgb_percent_to_hex(0.0, 1.0-percent, percent)
+    end
+
+    @colors = {}
+    @scores = {
+      'A' => 0.66,
+      'C' => 1.19,
+      'D' => 1.46,
+      'E' => 0.74,
+      'F' => 0.6,
+      'G' => 1.56,
+      'H' => 0.95,
+      'I' => 0.47,
+      'K' => 1.01,
+      'L' => 0.59,
+      'M' => 0.6,
+      'N' => 1.56,
+      'P' => 1.52,
+      'Q' => 0.98,
+      'R' => 0.95,
+      'S' => 1.43,
+      'T' => 0.96,
+      'U' => 0,
+      'V' => 0.5,
+      'W' => 0.96,
+      'Y' => 1.14,
+
+      'B' => 1.51,
+      'X' => 1.0,
+      'Z' => 0.86,
+    }
+    @min = 0.05
+    @max = 4.6
+    @scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
+    @colors.default = 'FFFFFF'  # return white by default
+
+  end
+end

data/lib/bio/util/color_scheme/helix.rb

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+#
+# bio/util/color_scheme/helix.rb - Color codings for helix propensity
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: helix.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+  class Helix < Score #:nodoc:
+
+    #########
+    protected
+    #########
+
+    def self.score_to_rgb_hex(score, min, max)
+      percent = score_to_percent(score, min, max)
+      rgb_percent_to_hex(percent, 1.0-percent, percent)
+    end
+
+    @colors = {}
+    @scores = {
+      'A' => 1.42,
+      'C' => 0.7,
+      'D' => 1.01,
+      'E' => 1.51,
+      'F' => 1.13,
+      'G' => 0.57,
+      'H' => 1.0,
+      'I' => 1.08,
+      'K' => 1.16,
+      'L' => 1.21,
+      'M' => 1.45,
+      'N' => 0.67,
+      'P' => 0.57,
+      'Q' => 1.11,
+      'R' => 0.98,
+      'S' => 0.77,
+      'T' => 0.83,
+      'U' => 0.0,
+      'V' => 1.06,
+      'W' => 1.08,
+      'Y' => 0.69,
+
+      'B' => 0.84,
+      'X' => 1.0,
+      'Z' => 1.31,
+    }
+    @min = 0.57
+    @max = 1.51
+    @scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
+    @colors.default = 'FFFFFF'  # return white by default
+
+  end
+end

data/lib/bio/util/color_scheme/hydropathy.rb

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+#
+# bio/util/color_scheme/hydropathy.rb - Color codings for hydrophobicity
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: hydropathy.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+
+  # Hydropathy index
+  # Kyte, J., and Doolittle, R.F., J. Mol. Biol.
+  # 1157, 105-132, 1982
+
+  class Hydropathy < Score #:nodoc:
+
+    #########
+    protected
+    #########
+
+    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' => 1.8,
+      'C' => 2.5,
+      'D' => -3.5,
+      'E' => -3.5,
+      'F' => 2.8,
+      'G' => -0.4,
+      'H' => -3.2,
+      'I' => 4.5,
+      'K' => -3.9,
+      'L' => 3.8,
+      'M' => 1.9,
+      'N' => -3.5,
+      'P' => -1.6,
+      'Q' => -3.5,
+      'R' => -4.5,
+      'S' => -0.8,
+      'T' => -0.7,
+      'U' => 0.0,
+      'V' => 4.2,
+      'W' => -0.9,
+      'Y' => -1.3,
+
+      'B' => -3.5,
+      'X' => -0.49,
+      'Z' => -3.5,
+    }
+    @min = -3.9
+    @max = 4.5
+    @scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
+    @colors.default = 'FFFFFF'  # return white by default
+
+  end
+end

data/lib/bio/util/color_scheme/nucleotide.rb

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+#
+# bio/util/color_scheme/nucleotide.rb - Color codings for nucleotides
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: nucleotide.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+  class Nucleotide < Simple #:nodoc:
+
+    #########
+    protected
+    #########
+
+    @colors = {
+      'A' => '64F73F',
+      'C' => 'FFB340',
+      'G' => 'EB413C',
+      'T' => '3C88EE',
+      'U' => '3C88EE',
+    }
+    @colors.default = 'FFFFFF'  # return white by default
+
+  end
+  NA = Nuc = Nucleotide
+end

data/lib/bio/util/color_scheme/strand.rb

@@ -0,0 +1,59 @@
+#
+# bio/util/color_scheme/strand.rb - Color codings for strand propensity
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: strand.rb,v 1.5 2007/04/05 23:35:41 trevor Exp $
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+  class Strand < Score #:nodoc:
+
+    #########
+    protected
+    #########
+
+    def self.score_to_rgb_hex(score, min, max)
+      percent = score_to_percent(score, min, max)
+      rgb_percent_to_hex(percent, percent, 1.0-percent)
+    end
+
+    @colors = {}
+    @scores = {
+      'A' => 0.83,
+      'C' => 1.19,
+      'D' => 0.54,
+      'E' => 0.37,
+      'F' => 1.38,
+      'G' => 0.75,
+      'H' => 0.87,
+      'I' => 1.6,
+      'K' => 0.74,
+      'L' => 1.3,
+      'M' => 1.05,
+      'N' => 0.89,
+      'P' => 0.55,
+      'Q' => 1.1,
+      'R' => 0.93,
+      'S' => 0.75,
+      'T' => 1.19,
+      'U' => 0.0,
+      'V' => 1.7,
+      'W' => 1.37,
+      'Y' => 1.47,
+
+      'B' => 0.72,
+      'X' => 1.0,
+      'Z' => 0.74,
+    }
+    @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
+end