//  $Id: CodonInfo.java,v 1.1 2006/05/20 17:02:03 Sasha Buzko Exp $
//
//  Copyright (c) 2000-2002  San Diego Supercomputer Center (SDSC),
//  a facility operated jointly by the University of California,
//  San Diego (UCSD) and General Atomics, San Diego, California, USA.
//
//  Users and possessors of this source code are hereby granted a
//  nonexclusive, royalty-free copyright and design patent license to
//  use this code in individual software.  License is not granted for
//  commercial resale, in whole or in part, without prior written
//  permission from SDSC.  This source is provided "AS IS" without express
//  or implied warranty of any kind.
//
//  For further information, please see:  http://mbt.sdsc.edu
//
//  History:
//  $Log: CodonInfo.java,v $
//  Revision 1.1  2006/05/20 17:02:03  Sasha Buzko
//  Updated version
//
//  Revision 1.1  2006/04/30 20:13:59  Sasha Buzko
//  New version of the app
//
//  Revision 1.1  2006/04/15 19:42:27  Sasha Buzko
//  Initial commit
//
//  Revision 1.1  2005/11/13 04:35:05  Administrator
//  *** empty log message ***
//
//  Revision 1.1.1.1  2002/07/16 18:00:21  moreland
//  Imported sources
//
//  Revision 1.0  2002/06/10 23:38:39  moreland
//


package edu.sdsc.mbt.util;


/**
 *  Provides static information about mRNA Codons such nucleic acid tuple
 *  / amino acid code mapping.
 *  <P>
 *  @see edu.sdsc.mbt.Residue
 *  @see edu.sdsc.mbt.util.AminoAcidInfo
 *  @see edu.sdsc.mbt.util.NucleicAcidInfo
 *  <P>
 *  @author John L. Moreland
 */
public class CodonInfo
{
	/**
	 *  A 2D storage array for nucleic acid tuple / amino acid code mapping.
	 *  <P>
	 *  codons[0][][] is the 1st letter of the nucleic acid codon 3-tuple.
	 *  codons[][0][] is the 2nd letter of the nucleic acid codon 3-tuple.
	 *  codons[][][0] is the 3rd letter of the nucleic acid codon 3-tuple.
	 *  codons[i][j][k] is the amino acid character code.
	 */
	private static final String codons[][][] =
	{
		// 1st letter = U
		{
			// 2nd letter = U
			{ "F", "F", "L", "L" },  // 3rd letter = U, C, A, G
			// 2nd letter = C
			{ "S", "S", "S", "S" },  // 3rd letter = U, C, A, G
			// 2nd letter = A
			{ "Y", "Y", ".", "." },  // 3rd letter = U, C, A, G
			// 2nd letter = G
			{ "C", "C", ".", "W" }   // 3rd letter = U, C, A, G
		},
		// 1st letter = C
		{
			// 2nd letter = U
			{ "L", "L", "L", "L" },  // 3rd letter = U, C, A, G
			// 2nd letter = C
			{ "P", "P", "P", "P" },  // 3rd letter = U, C, A, G
			// 2nd letter = A
			{ "H", "H", "Q", "Q" },  // 3rd letter = U, C, A, G
			// 2nd letter = G
			{ "R", "R", "R", "R" }   // 3rd letter = U, C, A, G
		},
		// 1st letter = A
		{
			// 2nd letter = U
			{ "I", "I", "I", "I" },  // 3rd letter = U, C, A, G
			// 2nd letter = C
			{ "T", "T", "T", "T" },  // 3rd letter = U, C, A, G
			// 2nd letter = A
			{ "B", "B", "K", "K" },  // 3rd letter = U, C, A, G
			// 2nd letter = G
			{ "S", "S", "R", "R" }   // 3rd letter = U, C, A, G
		},
		// 1st letter = G
		{
			// 2nd letter = U
			{ "V", "V", "V", "V" },  // 3rd letter = U, C, A, G
			// 2nd letter = C
			{ "A", "A", "A", "A" },  // 3rd letter = U, C, A, G
			// 2nd letter = A
			{ "D", "D", "E", "E" },  // 3rd letter = U, C, A, G
			// 2nd letter = G
			{ "G", "G", "G", "G" }   // 3rd letter = U, C, A, G
		}
	};

	private static final int getBaseIndex( char letter )
	{
		if ( letter == 'U' ) return 0;
		if ( letter == 'C' ) return 1;
		if ( letter == 'A' ) return 2;
		if ( letter == 'G' ) return 3;
		return -1;
	}

	private static final String letters[] = { "U", "C", "A", "G" };
	private static final String getBaseLetter( int index )
	{
		if ( index < 0 ) return null;
		if ( index > letters.length ) return null;
		return letters[index];
	}

	/**
	 *  Returns the number of codon/amino-acid tuples in the database.
	 *  <P>
	 */
	public static int getCodonCount( )
	{
		return 64; // There are 64 3-tuple mRNA codons.
	}

	/**
	 *  Returns the amino acid letter code for the given 3-letter codon
	 *  tuple.
	 *  <P>
	 */
	public static String getAminoAcidLetter( String codon )
	{
		if ( codon == null ) return null;

		int i = getBaseIndex( codon.charAt(0) );
		int j = getBaseIndex( codon.charAt(1) );
		int k = getBaseIndex( codon.charAt(2) );

		if ( (i < 0) || (j < 0) || (k < 0) ) return null;
		if ( i >= codons.length ) return null;
		if ( j >= codons[i].length ) return null;
		if ( k >= codons[i][j].length ) return null;

		return codons[i][j][k];
	}

	/**
	 *  Returns the amino acid letter code for the given 3-letter codon
	 *  tuple.
	 *  <P>
	 */
	public static String getAminoAcidLetter( String letter1, String letter2, String letter3 )
	{
		if ( letter1 == null ) return null;
		if ( letter2 == null ) return null;
		if ( letter3 == null ) return null;

		int i = getBaseIndex( letter1.charAt(0) );
		int j = getBaseIndex( letter2.charAt(0) );
		int k = getBaseIndex( letter3.charAt(0) );

		if ( (i < 0) || (j < 0) || (k < 0) ) return null;
		if ( i >= codons.length ) return null;
		if ( j >= codons[i].length ) return null;
		if ( k >= codons[i][j].length ) return null;

		return codons[i][j][k];
	}
}