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Alignments.

Simple alignment API (Yet Another Alignment API, YAAA) offering data structures for Ontology Alignments as well as additional alignment-related services.

This module contains means to visualize Alignments. The most important interface is the Visualizer class. A trivial implementation (essentially just using toString()) is the StringVisualizer. A more sophisticated example that is recommended for outside use is the HTMLVisualizer. All other classes are helper classes for said HTMLVisualizer.

This module provides algorithms to compare sets, that is, order-invariant lists. These algorithms are implementations of the AlignmentAlgorithm interface defined in the algorithms module. In particular, this module contains the StrictSetAlignmentScoreAlgorithm for computing the cost of the optimal unordered alignment of two sets, the StrictSetAlignmentFullAlgorithm which provides the Alignment itself as well, and the GreedySetAlignmentScoreAlgorithm as well as the GreedySetAlignmentFullAlgorithm for computing a potentially sub-optimal but faster alignment of two sets. The optimal alignments rely on the HungarianAlgorithm for solving the assignment problem in bipartite graphs. Here, we rely on the implementation provided by Kevin L. Stern which is provided within this distribution.

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.

This module contains a more general approach to construct AlignmentAlgorithms by relying on the theoretical concept of Algebraic Dynamic Programming (ADP) as developed by Giegerich et al. ADP defines four ingredients for an alignment algorithm: 1.) A signature that defines the permitted alignment operations. Operations are just function templates with an associated arity, meaning the number of arguments it takes from the left sequence and from the right sequence. In the TCSAlignmentToolbox we have a fixed signature with the following operations: REPLACEMENT(1, 1), DELETION(1, 0), INSERTION(0, 1), SKIPDELETION(1, 0) and SKIPINSERTION(0, 1) 2.) A regular tree grammar that produces alignments, that is: sequences of operations, in a restricted fashion. 3.) An algebra that can translate such trees to a cost. In the TCSAlignmentToolbox this is a Comparator. 4.) A choice function, in case of the TCSAlignmentToolbox: the strict minimum or the soft minimum. An alignment algorithm in the TCSAlignmentToolbox sense of the word then is the combination of choice function and grammar. While we provide hardcoded versions of these combinations in the main package, the adp package allows you to create your own grammars. You can combine them with a choice function by instantiating one of the Algorithm classes provided in this package with a grammar of your choice. For example: AlignmentAlgorithm algo = new SoftADPScoreAlgorithm(my_grammar, comparator); creates an alignment algorithm that implicitly produces all possible alignments your grammar can construct with the given input, translates them to a cost using the algebra/comparator you provided and applies the soft minimum to return the score. This all gets efficient by dynamic programming. Note that there is runtime overhead when using this method in comparison with the hardcoded algorithms. But for complicated grammars this is a much easier way to go. For more information on the theory, please refer to my master's thesis: "Adaptive Affine Sequence Alignment using Algebraic Dynamic Programming"