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

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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;

import de.citec.tcs.alignment.sequence.Sequence;

/**
 * This is the most generic AlignmentAlgorithm interface for all algorithms
 * that provide some sort of alignment between two input sequences.
 *
 * @author Benjamin Paassen - [email protected]
 * @param  the result class that represents the alignment in some way.
 */
public interface AlignmentAlgorithm {

	/**
	 * This should return the specification that is used for this Algorithm.
	 *
	 * @return the specification that is used for this Algorithm.
	 */
	public AlignmentSpecification getSpecification();

	/**
	 * This calculates the alignment between the Sequences a and b and returns
	 * it as an instance of the result class for this algorithm.
	 *
	 * Specific parameters should be set either in the AlignmentSpecification or
	 * in the Algorithm itself.
	 *
	 * Furthermore, this implementation should garantuee that
	 * A symmetric scoring scheme in the comparators leads to symmetric
	 * distances, meaning that calculateAlignment(a,b) =
	 * calculateAlignment(b,a)
	 * The replacement cost between two nodes a_i and b_j is defined as the
	 * weighted sum over all comparator distances.
	 * The self distance calculateAlignment(a,a) is scored with
	 * approximately 0.
         * The worst possible distance is 1.
	 *
	 * @param a The first sequence.
	 * @param b The second sequence.
	 *
	 * @return An alignment of a and b in terms of the given result class.
	 */
	public R calculateAlignment(Sequence a, Sequence b);

	/**
	 * This method shall return the class of the alignment result.
	 *
	 * @return the class of the alignment result.
	 */
	public Class getResultClass();

}