Download de.cit-ec.tcs.alignment JAR files with all dependencies

This module contains a library of standard implementations of Comparators and Normalizers as defined in the comparators module.

This module provides a very basic support for the parallel computing of tasks (Engine class) and entries of a matrix (MatrixEngine). This is basically just a wrapper around the java standard functionality for parallel computing (mainly the Standard Thread Pool and the Future interface). Additional functionality is provided by the ProgressReporter interface, which can be used as a hook to provide information on the current state of the parallel computing task to other modules or the user.

This module is a custom implementation of the Large Margin Nearest Neighbor classification scheme of Weinberger, Saul, et al. (2009). It contains an implementation of the k-nearest neighbor and LMNN classifier as well as (most importantly) gradient calculation schemes on the LMNN cost function given a sequential data set and a user-choice of alignment algorithm. This enables users to learn parameters of the alignment distance in question using a gradient descent on the LMNN cost function. More information on this approach can be found in the Masters Thesis "Adaptive Affine Sequence Alignment Using Algebraic Dynamic Programming"

This module contains convenience functions to interface with primitive datatypes more comfortably.

This module provides two packages, 'trees' and 'forests', which provide algorithms to compute edit distances on trees and forests (that is, unordered or ordered lists of trees) respectively. The edit distance is computed according to the tree edit distance algorithm of Zhang and Shasha (1989). The basic tree data structure is defined by the Tree interface in the trees module. Please refer to the javadoc for more detailed information.

This module defines the interfaces for Comparators in the TCS Alignment Toolbox. A Comparator has the purpose of defining the dissimilarity between elements in the input sequences of an Alignment. More specific information on Comparators can be found in the 'Comparator' interface. You can find a lot of helpful standard implementations of Comparators in the comparators-lib module. In the TCS Alignment Toolbox we require the output values of Comparators to lie in the range [0,1]. Many natural dissimilarities on value sets do not meet this criterion, such that additional normalization has to be applied. To that end this package also contains a Normalizer interface for functions that map real values from the range [0, infinity) to the range [0,1]. This package also provides a few convenience implementations of the Comparator interface to make the implementation of custom Comparators simpler, namely: SkipExtendedComparator, ParameterLessSkipExtendedComparator, ComparisonBasedSkipExtendedComparator, and ParameterLessComparisonBasedSkipExtendedComparator. Finally the TCS Alignment Toolbox also provides the means to learn parameters of Comparators. To enable that Comparators must implement the DerivableComparator interface to properly define the parameters that can be learned and the gradient of the dissimilarity with respect to these parameters. Gradients are stored using the Gradient interface as well as some convenience implementations of said interface, namely EmptyGradient, SingletonGradient, ArrayGradient and ListGradient.

This module permits exporting and importing of Sequence objects to CSV files. The underlying NodeSpecification is stored via a JSON file. The module aims at human- readable and compatible storage. For storage efficiency, further compression is advised.

This module contains some wrappers to make usage of the TCSAlignmentToolbox easier. Most important for beginners is the StringEditDistance, which provides convenience functions for simple string comparisons. For sequences of vectors we provide the VectorialSequences wrapper. The RandomSequenceGenerator enables you to generate random multi-modal sequences for testing purposes.

This module contains convenience functions to interface with primitive datatypes more comfortably.

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.