de.citec.tcs.alignment.CooptimalModel Maven / Gradle / Ivy

Go to download
/* 
 * TCS Alignment Toolbox Version 3
 * 
 * Copyright (C) 2016
 * Benjamin Paaßen
 * 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;

import de.citec.tcs.alignment.comparators.Comparator;
import de.citec.tcs.alignment.comparators.DerivableComparator;
import de.citec.tcs.alignment.comparators.OperationType;
import de.citec.tcs.alignment.parallel.MatrixEngine;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import lombok.Getter;
import lombok.NonNull;

/**
 * This is a sparse model of all co-optimal paths in an alignment matrix. It essentially stores for
 * every partial sequences of both input sequences the co-optimal operations that could have been
 * applied.
 *
 * @author Benjamin Paassen - bpaassen(at)techfak.uni-bielefeld.de
 * @param  the class of the elements in the left input sequence.
 * @param  the class of the elements in the right input sequence.
 */
public class CooptimalModel implements DerivableAlignmentDistance {

	/**
	 * The Comparator that was used to compute this CooptimalModel.
	 *
	 * @return The Comparator that was used to compute this CooptimalModel.
	 */
	@Getter
	@NonNull
	private final Comparator comparator;
	@NonNull
	private final List left;
	@NonNull
	private final List right;
	private final double distance;
	@NonNull
	private final TreeMap cooptimals = new TreeMap<>();

	public CooptimalModel(@NonNull final Comparator comparator,
			@NonNull final List left, @NonNull final List right,
			final double distance) {
		this.comparator = comparator;
		this.left = left;
		this.right = right;
		this.distance = distance;
	}

	/**
	 * A Map of matrix coordinates to an array of sequences of operations that can be co-optimally
	 * applied at the given position of the dynamic programming matrix.
	 *
	 * @return A Map of matrix coordinates to an array of sequences of operations that can be
	 * co-optimally applied at the given position of the dynamic programming matrix.
	 */
	public Map getCooptimals() {
		return cooptimals;
	}

	@Override
	public List getLeft() {
		return left;
	}

	@Override
	public List getRight() {
		return right;
	}

	@Override
	public double getDistance() {
		return distance;
	}

	@Override
	public double[] computeGradient(@NonNull DerivableComparator comp) {
		//TODO: This should be implemented at some point.
		throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
	}
}