/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.core.sequence.template;

import org.biojava.nbio.core.sequence.compound.NucleotideCompound;

import java.util.*;

/**
 *
 * @author Andy Yates
 * @param <C> Type of compound this set will contain but must extend
 * NucleotideCompound
 */
public abstract class AbstractNucleotideCompoundSet<C extends NucleotideCompound>
	extends AbstractCompoundSet<C> {

	protected void addNucleotideCompound(String base, String complement, String... equivalents) {

		String[] upperEquivalents = new String[equivalents.length];
		String[] lowerEquivalents = new String[equivalents.length];
		for(int i=0; i<equivalents.length; i++) {
			upperEquivalents[i] = equivalents[i].toUpperCase();
			lowerEquivalents[i] = equivalents[i].toLowerCase();
		}

		C upper = newNucleotideCompound(base.toUpperCase(), complement.toUpperCase(), upperEquivalents);
		C lower = newNucleotideCompound(base.toLowerCase(), complement.toLowerCase(), lowerEquivalents);

		List<C> equivalentCompounds = new ArrayList<C>();

		for(int i=0; i<equivalents.length; i++) {
			equivalentCompounds.add(getCompoundForString(upperEquivalents[i]));
			equivalentCompounds.add(getCompoundForString(lowerEquivalents[i]));
		}

		addCompound(upper, lower, equivalentCompounds);
	}

	protected abstract C newNucleotideCompound(String base, String complement, String... equivalents);

	/**
	 * Loops through all known nucleotides and attempts to find which are
	 * equivalent to each other. Also takes into account lower casing
	 * nucleotides as well as upper-cased ones.
	 */
	@SuppressWarnings("unchecked")
	protected void calculateIndirectAmbiguities() {
		Map<NucleotideCompound, List<NucleotideCompound>> equivalentsMap = new HashMap<NucleotideCompound, List<NucleotideCompound>>();

		List<NucleotideCompound> ambiguousCompounds = new ArrayList<NucleotideCompound>();
		for(NucleotideCompound compound: getAllCompounds()) {
			if (!compound.isAmbiguous()) {
				continue;
			}
			ambiguousCompounds.add(compound);
		}

		for(NucleotideCompound sourceCompound: ambiguousCompounds) {
			Set<NucleotideCompound> compoundConstituents = sourceCompound.getConstituents();
			for(NucleotideCompound targetCompound: ambiguousCompounds) {
				Set<NucleotideCompound> targetConstituents = targetCompound.getConstituents();
				if(targetConstituents.containsAll(compoundConstituents)) {
					NucleotideCompound lcSourceCompound = toLowerCase(sourceCompound);
					NucleotideCompound lcTargetCompound = toLowerCase(targetCompound);

				//equivalentsMap.put(sourceCompound, targetCompound);
			//      equivalentsMap.put(sourceCompound, lcTargetCompound);


					checkAdd(equivalentsMap, sourceCompound, targetCompound);
					checkAdd(equivalentsMap, sourceCompound, lcTargetCompound);

					checkAdd(equivalentsMap,targetCompound,sourceCompound);
					checkAdd(equivalentsMap, lcTargetCompound, sourceCompound);

					checkAdd(equivalentsMap, lcSourceCompound, targetCompound);
					checkAdd(equivalentsMap, lcSourceCompound, lcTargetCompound);

				}
			}
		}

		//And once it's all done start adding them to the equivalents map

		for ( NucleotideCompound key: equivalentsMap.keySet()){
			List<NucleotideCompound> vals = equivalentsMap.get(key);
			for (NucleotideCompound value: vals){
				addEquivalent((C)key,(C)value);
				addEquivalent((C)value,(C)key);
			}
		}
	}

	private void checkAdd(
		Map<NucleotideCompound, List<NucleotideCompound>> equivalentsMap,
		NucleotideCompound key,
		NucleotideCompound value) {


			List<NucleotideCompound> listS = equivalentsMap.get(key);
			if ( listS == null){
				listS = new ArrayList<NucleotideCompound>();
				equivalentsMap.put(key, listS);
			}
			listS.add(value);


}

private NucleotideCompound toLowerCase(NucleotideCompound compound) {
		return getCompoundForString(compound.getBase().toLowerCase());
	}

	/**
	 * Calculates the best symbol for a collection of compounds. For example
	 * if you gave this method a AC it will return a M which is the ambiguity
	 * symbol for these compounds.
	 *
	 * @param compounds Compounds to calculate ambiguity for
	 * @return The ambiguity symbol which represents this set of nucleotides best
	 */
	public NucleotideCompound getAmbiguity(NucleotideCompound... compounds) {
		Set<NucleotideCompound> settedCompounds = new HashSet<NucleotideCompound>();
		for(NucleotideCompound compound: compounds) {
			for(NucleotideCompound subCompound: compound.getConstituents()) {
				settedCompounds.add(getCompoundForString(subCompound.getBase().toUpperCase()));
			}
		}
		for(NucleotideCompound compound: getAllCompounds()) {
			if(compound.getConstituents().equals(settedCompounds)) {
				return compound;
			}
		}
		return null;
	}

		/**
		 * NucleotideCompounds can always complement
		 */
		@Override
		public boolean isComplementable() {
				return true;
		}
}
