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/* 
 * TCS Alignment Toolbox
 * 
 * Copyright (C) 2013-2015
 * Benjamin Paaßen, Georg Zentgraf
 * AG Theoretical Computer Science
 * Centre of Excellence Cognitive Interaction Technology (CITEC)
 * University of Bielefeld
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 * 
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see .
 */
package de.citec.tcs.alignment.adp;

import de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar.Nonterminal;
import de.citec.tcs.alignment.comparators.OperationType;
import java.util.ArrayList;
import java.util.EnumSet;

/**
 * This is a slight variation of the global alignment grammar.
 * It enforces that deletions come before insertions and thereby limits the
 * search space a little. It also prevents semantic ambiguity as described by
 * Giegerich et al.
 *
 * Consider the two input sequences "a" and "b". The global alignment grammar
 * then permits both these alignments:
 *
 * DELETION('a', INSERTION(end, 'b'))
 * INSERTION(DELETION('a', end, 'b'))
 *
 * But these alignments are semantically equivalent. Therefore this grammar
 * does not allow the second alignment but only the first.
 *
 * This does not come with any runtime advantage, because the management of the
 * additional dynamic programming table comes with a higher cost than leaving
 * the additional candidates in the search space. However this grammar might
 * be interesting for derivative calculation as it changes the operations that
 * are used and does not over-emphasize deletions and insertions in comparison
 * to replacements.
 *
 * The GAP-L version of this grammar would be
 *
 * grammar gra_global_asym uses sig_alignment(axiom = ALI)
 * {
 *
 * ALI = del(, ALI) |
 * ins(, INS) |
 * rep(, ALI) |
 * nil() #h;
 *
 * INS = ins(, INS) |
 * rep(, ALI) |
 * nil() #h;
 * }
 *
 * @author Benjamin Paassen - bpaassen(at)techfak.uni-bielefeld.de
 */
public class GlobalAsymmetricGrammar implements Grammar {

	/**
	 * Creates an instance of the global, asymmetric grammar.
	 */
	public GlobalAsymmetricGrammar() {

	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public Nonterminal[] dependencySort() {
		return Nonterminal.values();
	}

	private final ProductionRule del
			= new ProductionRule<>(OperationType.DELETION, Nonterminal.ALI);
	private final ProductionRule ins
			= new ProductionRule<>(OperationType.INSERTION, Nonterminal.ALI);
	private final ProductionRule rep
			= new ProductionRule<>(OperationType.REPLACEMENT, Nonterminal.ALI);

	/**
	 * {@inheritDoc}
	 */
	@Override
	public ArrayList> getPossibleRules(
			Nonterminal nonterminal, int leftSize, int rightSize, int M, int N) {
		final ArrayList> rules = new ArrayList<>();
		if (leftSize > 0 && nonterminal == Nonterminal.ALI) {
			rules.add(del);
		}
		if (rightSize > 0) {
			rules.add(ins);
		}
		if (leftSize > 0 && rightSize > 0) {
			rules.add(rep);
		}
		return rules;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public boolean containsGaps() {
		return true;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public boolean containsSkips() {
		return false;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public Class getNonterminalClass() {
		return Nonterminal.class;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public Nonterminal getAxiom() {
		return Nonterminal.ALI;
	}

	private final EnumSet accepting = EnumSet.allOf(Nonterminal.class);

	/**
	 * {@inheritDoc}
	 */
	@Override
	public EnumSet getAccepting() {
		return accepting;
	}

	public static enum Nonterminal {

		ALI,
		INS
	}

}