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/* 
 * 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 .
 */
/**
 * This module defines the interface for AlignmentAlgorithms as well as some helper classes. An
 * AlignmentAlgorithm computes an Alignment of two given input sequences, given a Comparator that
 * works in these sequences.
 * More details on the AlignmentAlgorithm can be found in the respective interface. More information
 * on Comparators can be found in the comparators module.
 *
 * The resulting 'Alignment' may be just a real-valued dissimilarity between the input sequence or
 * may incorporate additional information, such as a full Alignment, a PathList, a PathMap or a
 * CooptimalModel. If those results support the calculation of a Gradient, they implement the
 * DerivableAlignmentDistance interface.
 *
 * In more detail, the Alignment class represents the result of a backtracing scheme, listing all
 * Operations that have been applied in one co-optimal Alignment.
 *
 * A classic AlignmentAlgorithm does not result in a differentiable dissimilarity, because the
 * minimum function is not differentiable. Therefore, this package also contains utility functions
 * for a soft approximation of the minimum function, namely Softmin.
 *
 * For faster (parallel) computation of many different alignments or gradients we also provide the
 * ParallelProcessingEngine, the SquareParallelProcessingEngine and the ParallelGradientEngine.
 *
 * @author Benjamin Paassen - [email protected]
 */
package de.citec.tcs.alignment;