bio 0.7.0

data/lib/bio/util/color_scheme.rb

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+module Bio
+
+#
+# bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
+#
+# Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+# License::    LGPL
+#
+#  $Id: color_scheme.rb,v 1.2 2005/12/13 14:58:07 trevor Exp $
+#
+#
+#--
+#
+#  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@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
+  # NOTE todo
+  # BLOSUM62
+  # ClustalX
+  # PID
+
+  # A very basic class template for color code referencing.
+  class Simple
+    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
+    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
+
+
+  # NOTE todo
+  class Consensus
+  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
+#
+# Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+# License::    LGPL
+#
+#  $Id: buried.rb,v 1.2 2005/12/13 14:58:07 trevor Exp $
+#
+#
+#--
+#
+#  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
+#
+#++
+#
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+  class Buried < Score
+
+    #########
+    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
+#
+# Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+# License::    LGPL
+#
+#  $Id: helix.rb,v 1.2 2005/12/13 14:58:07 trevor Exp $
+#
+#
+#--
+#
+#  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
+#
+#++
+#
+#
+
+require 'bio/util/color_scheme'
+
+module Bio::ColorScheme
+  class Helix < Score
+
+    #########
+    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

@@ -0,0 +1,83 @@
+#
+# bio/util/color_scheme/hydropathy.rb - Color codings for hydrophobicity
+#
+# Copyright::  Copyright (C) 2005 Trevor Wennblom <trevor@corevx.com>
+# License::    LGPL
+#
+#  $Id: hydropathy.rb,v 1.2 2005/12/13 14:58:07 trevor Exp $
+#
+#
+#--
+#
+#  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
+#
+#++
+#
+#
+
+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
+
+    #########
+    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