Module | Bio::ColorScheme
In: | lib/bio/util/color_scheme.rb lib/bio/util/color_scheme/buried.rb lib/bio/util/color_scheme/helix.rb lib/bio/util/color_scheme/hydropathy.rb lib/bio/util/color_scheme/nucleotide.rb lib/bio/util/color_scheme/strand.rb lib/bio/util/color_scheme/taylor.rb lib/bio/util/color_scheme/turn.rb lib/bio/util/color_scheme/zappo.rb

bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids

Author: | Trevor Wennblom <trevor@corevx.com>
Copyright: | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (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 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

### Constants

NA | = | Nuc = Nucleotide

[Validate]