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

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 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 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.