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This repository contains various third party sources required by the main retepTools repository. The reason for this is when they are only available in SNAPSHOT format and we require a release version to enable us to run a release. Although not ideal, this is sometimes necessary if some critical bug needs to be fixed. Currently this contains docbkx-tools. Rules for this repository: * Projects must follow the same licensing as the main project :- BSD, Apache2 etc but not GPL, LGPL etc * groupId's must be within the uk.org.retep.third-party namespace - and not the projects original namespace (so we don't have version conflicts) * Must be disabled/removed once those projects become stable

This subproject is an extension of the Struts tag library. Each JSP custom tag in this library is a subclass of an associated tag in the Struts tag library. One difference is that this tag library does not use "rtexprvalues", it uses the expression evaluation engine in the Jakarta Taglibs implementation of the JSP Standard Tag Library (version 1.0) to evaluate attribute values. In addition, some of the Struts tags were not ported to this library, as it was determined that their functionality was entirely supplied by the JSTL. These particular Struts tags, and the reason for their non-porting will be described in the documentation for this library. In order to fully understand the correct utilization of this library, you must understand the use and operation of the Struts tag library, and the use and operation of the JavaServer Pages Standard Tag Library (hereafter called the "JSTL"), along with the expression language (sometimes called the "EL") used for evaluating attribute values.

This project is a collection of miscellaneous tools shared by a number of projects of the same author. There are **simple tuples** to use with Java Streams, **type-safe maps** ([inspired by the heterogeneous map pattern](https://www.informit.com/articles/article.aspx?p=2861454&seqNum=8)) described in Effective Java by Joshua Bloch, a **finder** that handles in a smart way queries to data sources, a facility to use the **DCI (Data, Context and Interactions) architectural pattern**, a simple **message bus** suitable for using the pub-sub pattern inside an application, some **test utilities**, an **experimental actor framework** and a few other small things. Yes, the project name is a tribute to the [jazz standard with the same name](https://en.wikipedia.org/wiki/These_Foolish_Things_(Remind_Me_of_You)) by Maschwitz and Strachey.

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.

--------------------------------------------------------------------------- Version for VIVO 1.8 This uses the source and test code from the Version for VIVO 1.10, edited to make it compatible with VIVO 1.8. It also borrows some code from VIVO 1.10 itself, changes the package name to avoid conflicts, and adds it here. * Vitro 1.8 uses Jena 2, not Jena 3, and Commons Lang 2, not 3, so modify the "import" statements in the Data Distribution code accordingly. * Vitro 1.8 does not have a "...webapp.utils.sparqlrunner" package, so borrow the source from Vitro 1.10, move it to a different package (just for compatibility with the 1.9 version), modify it to use Jena 2 and Commons Lang 2, and modify the Data Distribution API code to use this sparqlrunner package. * Vitro 1.9 has an earlier version of "...webapp.utils.configuration" package, so borrow the source from Vitro 1.10, move it to a different package so it won't conflict with the 1.9 version, modify it to use Jena 2 and Commons Lang 2, and modify the Data Distribution API code to use this configuration package. Make these modifications, compile, JAR it up, and deploy. --------------------------------------------------------------------------- Because VIVO 1.8 is not available as a Maven package, we have extracted the class files, JARed them up, and stored them in a file-based repository within this project. But that doesn't include any transitive dependencies, so any package that this code requires must be explicitly listed as a dependency. ---------------------------------------------------------------------------

GroupDocs.Signature for Java allows developers to write applications with ability to significantly sign electronic docs and verify them. Signatures can be of different types. API supports multitude of file formats and includes Pdf, Microsoft Office documents, Open Office formats, PowerPoint presentations, Images etc. The quite captivating fact about the API is, its UI less and independent calls can be made. It also provides a useful features to verify signed documents with stored signatures. Signature Types: - Text Signature - Image Signature - Digital Signature - Barcode Signature - QR-Code Signature - Stamp Signature Verification Types: - Text Signature - Digital Signature - Barcode Signature - QR-Code Signature For more details on the library, please visit GroupDocs website at: http://groupdocs.com/products/signature/java Note: The library comes up with some limitations in the evaluation mode. In order to test full features of GroupDocs.Signature for Java library, please request a free 30-day temporary license.

All Gwt jre emulation code goes in this module, as well as any gwt-compiler overrides. xapi-gwt-api.jar must come before gwt-dev.jar on your compile classpath. A plugin is being built to automatically adjust maven runtime dependencies, but users of ant or IDEs will need to ensure the super jar comes before gwt-dev. We will petition gwt to accept our mods, but, until then, if you want bleeding edge features, you gotta do bleeding edge configuration. Code that ties directly into other modules, like java.lang.reflect for the reflection submodule, have their super-source here, and generators or other implementations in their own modules. This is to maintain consistency in what is or isn't whitelisted in XApi GWT. Some modules, like appengine, provide dependency-specific super-source in their own packages. This module is for jre, junit and core XApi services.

Xypron Statistics is a Java library which was developped with supply chain simulation in mind. The normal, the exponential and the gamma distribution have been included. Methods to calculate fill rate and order rate service levels as well as safety factors are provided. The Mersenne Twister algorithm is used to provide high quality random number generation. Some functions for the gamma distribution where adopted from http://www.ssfnet.org/download/ssfnet_raceway-2.0.tar.gz. For these the following applies: Copyright 1999 CERN - European Organization for Nuclear Research. Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty.

HermiT is reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more. This is the maven build of HermiT and is designed for people who wish to use HermiT from within the OWL API. It is not officially supported by the HermiT development team, but was built initially for use with the Clojure-OWL library. It is built using the HermiT source tree without modification. There have been some additions to the test source tree to account for differences between the maven and ant environment; these are small and (hopefully) maintainable. The version number of this package is a composite of the HermiT version and an value representing releases of this packaged version. So, 1.3.7.1 is the first release of the mavenized version of HermiT based on the 1.3.7 release of HermiT. This package includes the Jautomata library (http://jautomata.sourceforge.net/), and builds with it directly. This library appears to be no longer under active development, and so a "fork" seems appropriate. No development is intended or anticipated on this code base.