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package org.snpeff.codons;

import java.util.HashMap;
import java.util.Iterator;

import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Genome;

/**
 * All codon tables are stored here. Mapping for genome/chromosome to codon table are also stored here
 *
 * Note: This object is a singleton
 *
 * @author pcingola
 */
public class CodonTables implements Iterable {

	// Standard codon table
	public static final String STANDARD_TABLE = "TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G";
	public static final String STANDARD_TABLE_NAME = "Standard";

	private static final String KEY_SEPARATOR = "_";
	private static final CodonTables codonTables = new CodonTables();

	HashMap codonTableByName;
	HashMap genChr2codonTable;

	public static CodonTables getInstance() {
		return codonTables;
	}

	private CodonTables() {
		codonTableByName = new HashMap();
		genChr2codonTable = new HashMap();
		CodonTable codonTable = new CodonTable(STANDARD_TABLE_NAME, STANDARD_TABLE);
		add(codonTable);
	}

	/**
	 * Translate a codon into an amino acid for a given genome+chromosome
	 */
	public String aa(String codon, Genome genome, String chromosome) {
		return getTable(genome, chromosome).aa(codon);
	}

	/**
	 * Add a codon table
	 */
	public void add(CodonTable codonTable) {
		codonTableByName.put(codonTable.getName(), codonTable);
	}

	/**
	 * Translate an amino acid into a codon for a given genome+chromosome
	 */
	public String codon(String aa, Genome genome, String chromosome) {
		return getTable(genome, chromosome).codon(aa);
	}

	/**
	 * Get default genome-wide codon table
	 */
	public CodonTable getTable(Genome genome) {
		String key = genome.getId();
		CodonTable codonTable = genChr2codonTable.get(key);
		if (codonTable == null) return codonTables.getTable(STANDARD_TABLE_NAME); // Not found? Use default
		return codonTable;
	}

	/**
	 * Get a codon table
	 * WARNING: It will return the standard codon table if nothing if found
	 */
	public CodonTable getTable(Genome genome, String chromosome) {
		String key = genome.getId() + KEY_SEPARATOR + chromosome;
		CodonTable codonTable = genChr2codonTable.get(key);
		if (codonTable != null) return codonTable;
		return getTable(genome); // Not found? Use genome wide codon table
	}

	/**
	 * Get a codon table by name
	 */
	public CodonTable getTable(String codonTableName) {
		return getInstance().codonTableByName.get(codonTableName);
	}

	@Override
	public Iterator iterator() {
		return codonTableByName.values().iterator();
	}

	/**
	 * Set a codon table for a given genome & chromosome
	 */
	public void set(Genome genome, Chromosome chr, CodonTable codonTable) {
		add(codonTable); // Just in case it's not already added
		String key = genome.getId() + KEY_SEPARATOR + chr.getId();
		genChr2codonTable.put(key, codonTable);
	}

	/**
	 * Set a codon table for a all chromosomes in a genome
	 * I.e.: Default genome-wide chromosome table
	 */
	public void set(Genome genome, CodonTable codonTable) {
		add(codonTable); // Just in case it's not already added
		String key = genome.getId();
		genChr2codonTable.put(key, codonTable);
	}

}