//  $Id: InfoUtil.java,v 1.4 2004/04/08 23:55:06 moreland Exp $
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//  History:
//  $Log: InfoUtil.java,v $
//  Revision 1.4  2004/04/08 23:55:06  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.3  2004/01/30 02:07:36  moreland
//  Updated copyright and class block comments.
//
//  Revision 1.2  2003/01/27 20:45:18  moreland
//  Added code to example programs in order to support standardized command
//  line arguments for data-set loading from files, URLs or PDB-ID codes.
//
//  Revision 1.1  2002/10/24 17:24:21  moreland
//  Added new example programs which adhear to the improved Structure API.
//
//  Revision 1.1.1.1  2002/07/16 18:00:15  moreland
//  Imported sources
//
//  Revision 1.0  2002/06/10 23:38:39  moreland
//


import edu.sdsc.mbt.util.*;

/**
 *  Prints the genetic code mapping with long amino acid name for all
 *  known mRNA codons. Demonstrates some of the functionality of the
 *  NucleicAcidInfo, AminoAcidInfo, and CodonInfo utility classes.
 *  <P>
 *  4 mRNA nucleic acids --> 64 mRNA Codons --> 20 Amino Acids
 *  --> 16000+ proteins
 *  <P>
 *  @author	John L. Moreland
 *  @see	edu.sdsc.mbt.Residue
 */
public class InfoUtil
{
	public static void main( String args[] )
	{
		//
		// For each mRNA nucleic-acid base, construct an mRNA codon 3-tuple.
		//
		System.err.println( "InfoUtil.main: Codon --> Amino Acid" );
		String na_bases[] = NucleicAcidInfo.rna_bases;
		for ( int i=0; i<na_bases.length; i++ )
		{
			String letter1 = na_bases[i];
			for ( int j=0; j<na_bases.length; j++ )
			{
				String letter2 = na_bases[j];
				for ( int k=0; k<na_bases.length; k++ )
				{
					String letter3 = na_bases[k];

					//
					// Given an mRNA codon 3-tuple, get the amino acid
					// leter that it codes for.
					//
					String codon = letter1 + letter2 + letter3;
					String aa_letter = CodonInfo.getAminoAcidLetter( codon );

					//
					// Get the amino acid name from the amino acid letter.
					//
					String aa_name =
						AminoAcidInfo.getNameFromLetter( aa_letter );

					//
					// Print the results
					//
					System.err.println( "InfoUtil.main: " + codon +
						" --> " + aa_letter + " = " + aa_name );
				}
			}
		}
	}
}