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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.

ThreadFix is a software vulnerability aggregation and management system that reduces the time it takes to fix software vulnerabilities. ThreadFix imports the results from dynamic, static and manual testing to provide a centralized view of software security defects across development teams and applications. The system allows companies to correlate testing results and streamline software remediation efforts by simplifying feeds to software issue trackers. By auto generating application firewall rules, this tool allows organizations to continue remediation work uninterrupted. ThreadFix empowers managers with vulnerability trending reports that show progress over time, giving them justification for their efforts. ThreadFix is developed and maintained by Denim Group, Ltd (http://www.denimgroup.com) For information about commercial support and other services, contact Denim Group about ThreadFix http://www.denimgroup.com/resources-threadfix/

Beehive's goal is to make J2EE programming easier by building a simple object model on J2EE and Struts. Using the new JSR-175 annotations, Beehive reduces the coding necessary for J2EE. The initial Beehive project has three pieces. NetUI: An annotation-driven web application programming framework that is built atop Struts. NetUI centralizes navigation logic, state, metadata, and exception handling in a single encapsulated and reusable Page Flow Controller class. In addition, NetUI provides a set of JSP tags for rendering HTML / XHTML and higher-level UI constructs such as data grids and trees and has first-class integration with JavaServer Faces and Struts. Controls: A lightweight, metadata-driven component framework for building that reduces the complexity of being a client of enterprise resources. Controls provide a unified client abstraction that can be implemented to access a diverse set of enterprise resources using a single configuration model. In addition, Beehive includes a set of system controls that are abstractions for low-level J2EE resource APIs such as EJB, JMS, JDBC, and web services.