How do I make a CrossProductAlphabet such as a codon Alphabet? - Cookbook - BioSharp

CrossProductAlphabets result from the multiplication of other IAlphabets. CrossProductAlphabets are used to wrap up 2 or more Symbols into a single "cross product" ISymbol. For example using a 3 way cross of the DNA alphabet you could wrap a codon as a ISymbol. You could then count those codon ISymbols in a Count or you could used them in a Distribution.

CrossProductAlphabets can be created by name (if the component IAlphabets are registered in the AlphabetManager) or by making a list of the desired IAlphabets and creating the IAlphabet from the list. Both approaches are shown in the example below.


using System;
 
using BioSharp.Core.Utils;
using BioSharp.Core.Bio.Symbol;
using BioSharp.Core.Bio.Seq;
 
 
namespace Cookbook.Alphabets
{
    class CrossProduct
    {
        public static void Main(string[] args)
        {
            // Make a CrossProductAlphabet from a List
            EquatableList<IAlphabet> l = new EquatableList<IAlphabet>();
            l.Add(DNATools.DNA);
            l.Add(DNATools.DNA);
            l.Add(DNATools.DNA);
 
            IAlphabet codon = AlphabetManager.GetCrossProductAlphabet(l);
 
            // Get the same Alphabet by name
            IAlphabet codon2 = AlphabetManager.GenerateCrossProductAlphaFromName("(DNA x DNA x DNA)");
 
            // Show that the two Alphabets are canonical
            Console.WriteLine(codon == codon2);
        }
    }
}

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How do I make a CrossProductAlphabet such as a codon Alphabet? - Cookbook - BioSharp