Group: CIT EC TCS Alignment

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

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.

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.

This module containts standard implementations of AlignmentAlgorithms. In contrast to the adp module these implementations are hand-tailored for some specific algorithms and thus achieve somewhat faster runtime (a constant factor of maybe 30-50 ...

This module contains the sequence datastructure of the TCS Alignment Toolbox. It defines the possible value sets in the ValueType enum as well as the different KeywordSpecification classes, namely: 1.) StringKeywordSpecification for string type ...

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

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 ...

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.

This module contains means to visualize Alignments. The most important interface is the Visualizer class.

This module is a custom implementation of the Large Margin Nearest Neighbor classification scheme of Weinberger, Saul, et al. (2009).

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 ...

This module provides specializations of the Comparator interface for the Sequence data structure.

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.

This module permits exporting and importing of Sequence objects to CSV files. The underlying NodeSpecification is stored via a JSON file.

This module provides convenience implementations for visualization of the sequence datastructure.

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 ...