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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 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.

Multiple loosely coupled modules which extend ZK framework, originally created by DataLite company. ZKComposer - controll the MVC design with annotations @ZkEvent?, @ZkComponent?, @ZkBinding?, ... (similar to zkspring or zkcdi projects, however without any framework dependencies). ZKDLComponents splits ZK data driven components (listbox, combobox) to MVC design, adds support for easy large data manipulation and contains many pre-built user controls (filter manager, sort manager, visible listbox columns manager, export to excel, etc.) HibernateDAO & ZKDLComponentsHibernateExtensions - Hibernate generic DAO design with extensions for ZKDLComponents to replace all your plumbing code (filter, sort, lazy loading, CRUD). SpringService? - service layer with spring - generic service which speaks to generic DAO. This is the way we use our components at DataLite?, but you can use any integration or DAO at your will.

Multiple loosely coupled modules which extend ZK framework, originally created by DataLite company. ZKComposer - controll the MVC design with annotations @ZkEvent?, @ZkComponent?, @ZkBinding?, ... (similar to zkspring or zkcdi projects, however without any framework dependencies). ZKDLComponents splits ZK data driven components (listbox, combobox) to MVC design, adds support for easy large data manipulation and contains many pre-built user controls (filter manager, sort manager, visible listbox columns manager, export to excel, etc.) HibernateDAO & ZKDLComponentsHibernateExtensions - Hibernate generic DAO design with extensions for ZKDLComponents to replace all your plumbing code (filter, sort, lazy loading, CRUD). SpringService? - service layer with spring - generic service which speaks to generic DAO. This is the way we use our components at DataLite?, but you can use any integration or DAO at your will.